Soybean variety XB39Q15R

ABSTRACT

A novel soybean variety, designated XB39Q15R is provided. Also provided are the seeds of soybean variety XB39Q15R, cells from soybean variety XB39Q15R, plants of soybean XB39Q15R, and plant parts of soybean variety XB39Q15R. Methods provided include producing a soybean plant by crossing soybean variety XB39Q15R with another soybean plant, methods for introgressing a transgenic trait, a mutant trait, and/or a native trait into soybean variety XB39Q15R, methods for producing other soybean varieties or plant parts derived from soybean variety XB39Q15R, and methods of characterizing soybean variety XB39Q15R. Soybean seed, cells, plants, germplasm, breeding lines, varieties, and plant parts produced by these methods and/or derived from soybean variety XB39Q15R are further provided.

FIELD OF INVENTION

This invention relates generally to the field of soybean breeding,specifically relating to a soybean variety designated XB39Q15R.

BACKGROUND

The present invention relates to a new and distinctive soybean varietydesignated XB39Q15R, which has been the result of years of carefulbreeding and selection in a comprehensive soybean breeding program.There are numerous steps in the development of any novel, desirablesoybean variety. Plant breeding begins with the analysis and definitionof problems and weaknesses of the current germplasm, the establishmentof program goals, and the definition of specific breeding objectives.The next step is selection of germplasm that possess the traits to meetthe program goals. The breeder's goal is to combine in a single varietyan improved combination of desirable traits from the parental germplasm.These traits may include, but are not limited to: higher seed yield,resistance to diseases and/or insects, tolerance to drought and/or heat,altered fatty acid profile(s), abiotic stress tolerance, improvements incompositional traits, and better agronomic characteristics.

These product development processes, which lead to the final step ofmarketing and distribution, can take from six to twelve years from thetime the first cross is made until the finished seed is delivered to thefarmer for planting. Therefore, development of new varieties is atime-consuming process that requires precise planning, efficient use ofresources, and a minimum of changes in direction.

A continuing goal of soybean breeders is to develop stable, highyielding soybean varieties that are agronomically sound with maximalyield over one or more different conditions and environments.

SUMMARY

A novel soybean variety, designated XB39Q15R is provided. Also providedare the seeds of soybean variety XB39Q15R, cells from soybean varietyXB39Q15R, plants of soybean XB39Q15R, and plant parts of soybean varietyXB39Q15R. Methods provided include producing a soybean plant by crossingsoybean variety XB39Q15R with another soybean plant, methods forintrogressing a transgenic trait, a mutant trait, and/or a native traitinto soybean variety XB39Q15R, methods for producing other soybeanvarieties or plant parts derived from soybean variety XB39Q15R, andmethods of characterizing soybean variety XB39Q15R. Soybean seed, cells,plants, germplasm, breeding lines, varieties, and plant parts producedby these methods and/or derived from soybean variety XB39Q15R arefurther provided.

DETAILED DESCRIPTION Definitions

Certain definitions used in the specification are provided below. Also,in the examples and tables which follow, a number of terms are used. Inorder to provide a clear and consistent understanding of thespecification and claims, the following definitions are provided:

AERBLT=AWB=AERIAL WEB BLIGHT. Aerial web blight is caused by the fungusRhizoctonia solani, which can also cause seedling blight and root rot ofsoybeans. Stems, flowers, pods, petioles, and leaves are susceptible toformation of lesions. Tolerance to Aerial Web Blight is rated on a scaleof 1 to 9, relative to known checks, with a score of 1 beingsusceptible, and a score of 9 being tolerant. Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

ALLELE. Any of one or more alternative forms of a genetic sequence. In adiploid cell or organism, the two alleles of a given sequence typicallyoccupy corresponding loci on a pair of homologous chromosomes.

ANTHESIS. The time of a flower's opening.

ANTHRACNOSE. Anthracnose is a fungal disease commonly caused byColletotrichum truncatum, and in some cases other Colletotrichum speciesmay be involved. The fungus produces crowded, black acervuli on infectedtissues. These dark bodies typically look like pin cushions on thetissue surface when viewed under magnification. The most common symptomsare brown, irregularly shaped spots on stem, pods and petioles.Resistance is visually scored on a range from 1 to 9 comparing allgenotypes in a given experiment. A score of 9 indicates that there is noinfection (resistance). Preliminary scores are reported as doubledigits, for example ‘55’ indicates a preliminary score of 5 on the scaleof 1 to 9.

APHID ANTIBIOSIS. Aphid antibiosis is the ability of a variety to reducethe survival, growth, or reproduction of aphids that feed on it.Screening scores are based on the ability of the plant to decrease therate of aphid reproduction. Plants are compared to resistant andsusceptible check plants grown in the same experiment. Scores of1=susceptible, 3=below average, 5=average, 7=above average, and9=exceptional tolerance. Preliminary scores are reported as doubledigits, for example ‘55’ indicates a preliminary score of 5 on the scaleof 1 to 9.

APHID ANTIXENOSIS. Aphid antixenosis is a property of a variety toreduce the feeding of aphids upon the plant, this is also known asnonpreference. Screening scores are based on the ability of the plant todecrease the rate of aphid reproduction. Plants are compared toresistant and susceptible check plants grown in the same experiment.Scores of 1=susceptible plants covered with aphids, plants may showsevere damage such as stunting and/or necrosis, equivalent or worse whencompared to susceptible check, 3=below average, plants show major damagesuch as stunting and/or foliar necrosis, 5=moderately susceptible,7=above average, about 50 aphids on the plant, plant does not exhibitsigns of plant stress, and 9=exceptional tolerance, very few aphids onthe plant, equivalent or better when compared to a resistant check.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

BACKCROSSING. Process in which a breeder crosses a donor parent varietypossessing a desired trait or traits to a recurrent parent variety(which is agronomically superior but lacks the desired level or presenceof one or more traits) and then crosses the resultant progeny back tothe recurrent parent one or more times. Backcrossing can be used tointroduce one or more desired traits from one genetic background intoanother background that is lacking the desired traits.

BLUP=BEST LINEAR UNBIASED PREDICTION. The BLUP values are determinedfrom a mixed model analysis of variety performance observations atvarious locations and replications.

BREEDING. The genetic manipulation of living organisms, includingapplication of one or more agricultural and/or biotechnological tools,methods and/or processes to create useful new distinct varieties.

BU/A=Bushels per Acre. The seed yield in bushels/acre is the actualyield of the grain at harvest.

BROWN STEM ROT=BSR=Brown Stem Rot Tolerance. This is a visual diseasescore from 1 to 9 comparing all genotypes in a given test. The score isbased on symptoms on leaves and/or stems such as yellowing, necrosis,and on inner stem rotting caused by Phialophora gregata. A score of 1indicates severe symptoms of leaf yellowing and necrosis. Increasingvisual scores from 2 to 8 indicate additional levels of tolerance, whilea score of 9 indicates no symptoms. Preliminary scores are reported asdouble digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

BSRLF=Brown Stem Rot disease rating based solely on leaf diseasesymptoms. This is a visual disease score from 1 to 9 comparing allgenotypes in a given test. A score of 1 indicates severe leaf yellowingand necrosis. Increasing visual scores from 2 to 8 indicate additionallevels of tolerance, while a score of 9 indicates no leaf symptoms.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

BSRSTM=Brown Stem Rot disease rating based solely on stem diseasesymptoms. This is a visual disease score from 1 to 9 comparing allgenotypes in a given test. A score of 1 indicates severe necrosis on theinner stem tissues. Increasing visual scores from 2 to 8 indicateadditional levels of tolerance, while a score of 9 indicates no innerstem symptoms. Preliminary scores are reported as double digits, forexample ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

CELL. Cell as used herein includes a plant cell, whether isolated, intissue culture, or incorporated in a plant or plant part. The cell canbe a cell, such as a somatic cell, of the variety having the same set ofchromosomes as the cells of the deposited seed, or, if the cell containsa locus conversion or transgene, otherwise having the same oressentially the same set of chromosomes as the cells of the depositedseed.

CERK=CERCOSPORA TOLERANCE. A fungal disease caused by Cercosporakukuchii which can be identified by symptoms including one or more ofmottled reddish-purple discoloration of the uppermost leaves of thesoybean plant, mottled discoloration of leaf petioles, mottleddiscoloration of pods, and/or purple discoloration of the seed coat.Infected seed, having a purple discoloration, is commonly referred to aspurple seed stain. For the multiple expressions of this disease, plantsor plant parts are visually scored from 1 to 9 relative to picturediagrams for each trait. A score of 1 indicates severity of expression,while a score of 9 indicates no symptoms. Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

CRDC=CHARCOAL ROT DROUGHT COMPLEX=Charcoal Rot. A fungal disease causedby Macrophomina phaseolina that is enhanced by hot and dry conditions,especially during reproductive growth stages. Tolerance score is basedon field observations of the comparative ability to tolerate drought andlimit losses from charcoal rot infection among various soybeanvarieties. A score of 1 indicates severe charcoal rot on the roots anddark microsclerotia on the lower stem causing significant plant death.Increasing visual scores from 2 to 8 indicate additional levels oftolerance, while a score of 9 indicates no lower stem and/or root rotand no visual symptoms. Preliminary scores are reported as doubledigits, for example ‘55’ indicates a preliminary score of 5 on the scaleof 1 to 9.

CHLORIDE SALT TOLERANCE. This is a measure of the chloride saltconcentration in seedling plant tissue, arrayed on a scale based onchecks, and scores applied from 1 to 9. The higher the score the lowerthe concentration of chloride salts in the tissue measured. Preliminaryscores are reported as double digits, for example ‘55’ indicates apreliminary score of 5 on the scale of 1 to 9.

CW=Canopy Width. This is a visual observation of the canopy width whichis scored from 1 to 9 comparing all genotypes in a given test. A scoreof 1=very narrow, while a score of 9=very bushy.

CNKST=SOUTHERN STEM CANKER TOLERANCE. This is a visual disease scorefrom 1 to 9 comparing genotypes to standard checks chosen to arraydifferences. The score is based upon field reaction to the disease. Thecausative agent is Diaporthe phaseolorum var. meridionalis (SouthernStem Canker), which tends to impact southern geographic regions. A scoreof 1 indicates susceptibility to the disease, whereas a score of 9indicates the line is resistant to the disease. Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

CNKSG=SOUTHERN STEM CANKER GENETIC. This is a visual disease score from1 to 9 comparing genotypes to standard checks chosen to arraydifferences. The score is based upon toothpick bioassay in (1) field orshade tent bioassays or (2) controlled environmental chambers, and isbased on genetics that infers resistance or susceptibility to SouthernStem Canker. Diaporthe phaseollorum var. meridionalis is the causativeagent. A score of 1 indicates severe stem canker lesions, relative toknown susceptible check varieties, whereas a score of 9 indicates nomeaningful disease symptoms, consistent with known resistant checkvarieties. Preliminary scores are reported as double digits, for example‘99’ indicates a preliminary score of 9 on the scale of 1 to 9.

COTYLEDON. A cotyledon is a type of seed leaf. The cotyledon containsthe food storage tissues of the seed.

CROSS-POLLINATION. Fertilization by the union of two gametes fromdifferent plants.

DIPLOID. A cell or organism having two sets of chromosomes.

DM=DOWNY MILDEW. A fungal disease caused by Peronospora manshurica insoybean. Symptoms first appear on leaves, which can spread to podswithout obvious external symptoms, and further spread to seed. Infectedseed may have a dull white appearance. The tolerance score is based onobservations of symptoms on the leaves of plants regarding leaf damageand/or level of infection. On a scale of 1 to 9, a score of 1 indicatessevere symptoms, whereas a score of 9 indicates no disease symptoms.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

ELITE VARIETY. A variety that is sufficiently homozygous and homogeneousto be used for commercial grain production. An elite variety may also beused in further breeding.

EMBRYO. The embryo is the small plant contained within a mature seed.

EMGSC=Emergence Score=Field Emergence. A score based upon speed andstrength of emergence at sub-optimal conditions. Rating is done at theunifoliate to first trifoliate stages of growth. A score using a 1 to 9scale is given, with 1 being the poorest and 9 the best. Scores of 1, 2,and 3=degrees of unacceptable stands; slow growth and poor plant health.Scores of 4, 5, 6=degrees of less than optimal stands; moderate growthand plant health. Scores of 7, 8, 9=degrees of optimal stands; vigorousgrowth and plant health.

FEC=Iron-deficiency Chlorosis=Iron Chlorosis. Plants are scored 1 to 9based on visual observations. A score of 1 indicates the plants are deador dying from iron-deficiency chlorosis, a score of 5 means plants haveintermediate health with some leaf yellowing, and a score of 9 means nostunting of the plants or yellowing of the leaves. Preliminary scoresare reported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

FEY=FROGEYE LEAF SPOT. Frogeye Leaf Spot is a fungal disease caused byCercospora sojina. Plants are evaluated using a visual fungal diseasescore from 1 to 9 comparing all genotypes in a given trial to knownresistant and susceptible checks in the trial. The score is based uponthe number and size of leaf lesions. A score of 1 indicates severe leafnecrosis lesions, whereas a score of 9 indicates no lesions. Preliminaryscores are reported as double digits, for example ‘55’ indicates apreliminary score of 5 on the scale of 1 to 9.

FLOWER COLOR. Data values include: P=purple and W=white.

GENE SILENCING. The interruption or suppression of the expression of anucleic acid sequence at the level of transcription or translation.

GENOTYPE. Refers to the genetic constitution of a cell or organism.

GPC=Grams per hundred seeds=g/100 seeds. Soybean seeds vary in seedsize. The weight in grams of 100 seeds can be used to estimate the seedrequired to plant a given area. Seed size can also impact end uses.

PLANT GROWTH HABIT. This refers to the physical appearance of a plant.It can be determinate (DET), semi-determinate (SDET), or indeterminate(INDET). In soybeans, indeterminate varieties are those in which stemgrowth is not limited by formation of a reproductive structure (i.e.,flowers, pods and seeds) and hence growth continues throughout floweringand during part of pod filling. The main stem will develop and set podsover a prolonged period under favorable conditions. In soybeans,determinate varieties are those in which stem growth ceases at floweringtime. Most flowers develop simultaneously, and most pods fill atapproximately the same time. The terms semi-determinate and intermediateare also used to describe plant habit and are defined in Bernard, R. L.(1972) “Two genes affecting stem termination in soybeans.” Crop Science12:235-239; Woodworth, C. M. (1932) “Genetics and breeding in theimprovement of the soybean.” Bull. Agric. Exp. Stn. (Illinois)384:297-404; and Woodworth, C. M. (1933) “Genetics of the Soybean.” J.Am. Soc. Agron. 25:36-51.

HAPLOID. A cell or organism having one set of the two sets ofchromosomes in a diploid cell or organism.

HERBRES=Herbicide Resistance. This indicates that the plant is moretolerant to the herbicide or herbicide class shown as compared to thelevel of herbicide tolerance exhibited by wild type plants. Adesignation of ‘Gly’ indicates tolerance to glyphosate, a designation of‘SU’ indicates tolerance to sulfonylurea herbicides, a designation of‘ALS’ indicates tolerance to ALS-inhibiting herbicides, a designation of‘PPO’ indicates tolerance to protoporphyringogen oxidase (protox)inhibiting herbicides, a designation of ‘MET’ indicates tolerance tometribuzin, a designation of ‘AUX’ indicates tolerance to auxinherbicides, and a designation of ‘HPPD’ indicates tolerance top-hydroxyphenylpyruvate dioxygenase (HPPD) inhibiting herbicides. Adesignation of “ALS1” indicates that tolerance is conferred by thesoybean ALS1 gene, a designation of “ALS2” indicates that tolerance isconferred by the soybean ALS2 gene, and a designation of “HRA” indicatesthat tolerance is conferred by an HRA transgene.

HGT=Plant Height=Height/maturity. Plant height is taken from the top ofthe soil to the top pod of the plant and is measured in inches. Thescore is given on a scale of 1 to 9, with 9 being tall and 1 beingshort. The difference from one score to the next is approximately 2 to 3inches.

HIGH YIELD ENVIRONMENTS. Areas which lack normal stress, typicallyhaving sufficient rainfall, water drainage, low disease pressure, lowweed pressure, and/or uniform or low variability soil.

HILUM. This refers to the scar left on the seed which marks the placewhere the seed was attached to the pod prior to harvest. Hila Color datavalues include: BR=brown; TN=tan; Y=yellow; BL=black; IB=ImperfectBlack; BF=buff, G=Grey. Tan hila may also be designated as imperfectyellow (IY).

HLC=HO=High Oleic. Oil with seventy percent or more oleic acid isclassified as high oleic oil. Oleic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

HYPLSC=Hypocotyl length=Hypocotyl elongation. This score indicates theability of the seed to emerge when planted 3″ deep in sand pots and witha controlled temperature of 25° C. The number of plants that emerge eachday are counted. Based on this data, each genotype is given a score from1 to 9 based on its rate of emergence and the percent of emergence. Ascore of 1 indicates a very poor rate and percent of emergence, anintermediate score of 5 indicates average ratings, and a score of 9indicates an excellent rate and percent of emergence. Preliminary scoresare reported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

HYPOCOTYL. A hypocotyl is the portion of an embryo or seedling betweenthe cotyledons and the root.

HYPOCOTYL COLOR. This is the color of the hypocotyl taken approximately7 to 10 days after planting. Colors can be: G=green, GB=green withbronze, P=Purple, DP=dark purple.

LDGMID=Mid-Season Standability. The lodging resistance of plants at midseason. Lodging is rated on a scale of 1 to 9. A score of 1 indicatesplants that are lying on the ground, a score of 5 indicates plants areleaning at a 45° angle in relation to the ground, and a score of 9indicates erect plants. Preliminary scores may be reported as doubledigits, for example ‘55’ indicates a preliminary score of 5 on the scaleof 1 to 9.

LDGSEV=Lodging Resistance=Harvest Standability. Lodging is rated on ascale of 1 to 9. A score of 1 indicates plants that are lying on theground, a score of 5 indicates plants are leaning at a 45° angle inrelation to the ground, and a score of 9 indicates erect plants.Preliminary scores may be reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

LEAF COLOR: This is the color of the leaves taken at the R3 to R6 growthstage. Color ranges from light green, medium green and dark green.Number values are given on a scale of 1 to 9, with 1-3 being lightgreen, 4-6 being medium green and 7-9 being dark green.

LEAFLETS. These are parts of the plant shoot involved in the manufactureof food for the plant by the process of photosynthesis.

LINKAGE. Refers to a phenomenon wherein alleles on the same chromosometend to segregate together more often than expected by chance if theirtransmission was independent.

LINKAGE DISEQUILIBRIUM. Refers to a phenomenon wherein alleles tend toremain together in linkage groups when segregating from parents tooffspring, with a greater frequency than expected from their individualfrequencies.

LLC=Oil with three percent or less linolenic acid is classified as lowlinolenic oil. Linolenic acid is one of the five most abundant fattyacids in soybean seeds. It is measured by gas chromatography and isreported as a percent of the total oil content.

LLE=Linoleic Acid Percent. Linoleic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

LLN=Linolenic Acid Percent. Linolenic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

LOCUS. A defined segment of DNA.

LOCUS CONVERSION. Refers to seeds, plants, and/or parts thereofdeveloped by backcrossing wherein essentially all of the desiredmorphological and physiological characteristics of a variety arerecovered in addition to at least one locus which has been transferredinto the variety by introgression, backcrossing or transformation. Thelocus can be a native locus, a transgenic locus, or a combinationthereof.

MAT ABS=MATABS=ABSOLUTE MATURITY. This term is defined as the length oftime from planting to complete physiological development (maturity). Theperiod from planting until maturity is reached is measured in days,usually in comparison to one or more standard varieties. Plants areconsidered mature when 95% of the pods have reached their mature color.

MATURITY GROUP. This refers to an agreed-on industry division of groupsof varieties, based on the zones in which they are adapted primarilyaccording to day length or latitude. They consist of very long daylength varieties (Groups 000, 00, 0), and extend to very short daylength varieties (Groups VII, VIII, IX, X).

MST=Moisture at harvest. The actual percent of moisture in the soybeansat harvest.

NARROW ROWS. Term indicates 7″ and 15″ row spacing.

NEI DISTANCE. A quantitative measure of percent similarity between twolines. Nei's distance between lines A and B can be defined as1−((2*number alleles in common)/(number alleles in A+number alleles inB)). For example, if lines A and B are the same for 95 out of 100alleles, the Nei distance would be 0.05. If lines A and B are the samefor 98 out of 100 alleles, the Nei distance would be 0.02. Free softwarefor calculating Nei distance is available on the internet at multiplelocations. See Nei & Li (1979) Proc Natl Acad Sci USA 76:5269-5273,which is incorporated by reference for this purpose.

NUCLEIC ACID. An acidic, chain-like biological macromolecule consistingof multiple repeat units of phosphoric acid, sugar, and purine andpyrimidine bases.

OILPCT=% oil=OIL PERCENT=OIL (%). Soybean seeds contain a considerableamount of oil. Oil is measured by NIR spectrophotometry and is reportedas a percentage basis. The percent oil can be measured at a specifiedmoisture content of the seed, such as 13% moisture (H₂O).

OIL/MEAL TYPE. Designates varieties specially developed with thefollowing oil traits: HLC=High Oleic oil (≧70% oleic content); LLC=LowLinolenic (≦3% linolenic content); ULC=Ultra Low Linolenic oil (≦1%linolenic oil content).

OLC=OLEIC ACID PERCENT. Oleic acid is one of the five most abundantfatty acids in soybean seeds. It is measured by gas chromatography andis reported as a percent of the total oil content.

PEDIGREE DISTANCE. Relationship among generations based on theirancestral links as evidenced in pedigrees. May be measured by thedistance of the pedigree from a given starting point in the ancestry.

PERCENT IDENTITY. Percent identity as used herein refers to thecomparison of the homozygous alleles of two soybean varieties. Percentidentity is determined by comparing a statistically significant numberof the homozygous alleles of two developed varieties. For example, apercent identity of 90% between soybean variety 1 and soybean variety 2means that the two varieties have the same allele at 90% of the lociused in the comparison.

PERCENT SIMILARITY. Percent similarity as used herein refers to thecomparison of the homozygous alleles of a soybean variety such asXB39Q15R with another plant, and if the homozygous allele of XB39Q15Rmatches at least one of the alleles from the other plant, then they arescored as similar. Percent similarity is determined by comparing astatistically significant number of loci and recording the number ofloci with similar alleles as a percentage. A percent similarity of 90%between XB39Q15R and another plant means that XB39Q15R matches at leastone of the alleles of the other plant at 90% of the loci used in thecomparison.

PLANT. As used herein, the term “plant” includes reference to animmature or mature whole plant, including a plant from which seed orgrain or anthers have been removed. Any seed or embryo that will producethe plant is also considered to be the plant.

PLANT PARTS. As used herein, the term “plant parts” includes leaves,stems, roots, root tips, anthers, seed, grain, embryos, pollen, ovules,flowers, cotyledon, hypocotyl, pod, flower, shoot, stalk, tissue, tissuecultures, cells and the like.

PLM or PALMITIC ACID PERCENT. Palmitic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

PMG infested soils. Soils containing Phytophthora sojae.

POD. This refers to the fruit of a soybean plant. It consists of thehull or shell (pericarp) and the soybean seeds. Pod Color data valuesinclude: BR=brown; TN=tan.

POWDERY MILDEW. Powdery Mildew is caused by a fungus, Microsphaeradiffusa. Tolerance to Powdery Mildew is rated on a scale of 1 to 9, witha score of 1 being very susceptible ranging up to a score of 9 beingtolerant. Preliminary scores are reported as double digits, for example‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

PRM=PRMMAT=Predicted Relative Maturity=RM=Relative Maturity. Soybeanmaturities are divided into relative maturity groups (denoted as 000,00, 0, I, II, III, IV, V, VI, VII, VIII, IX, X, or 000, 00, 0, 1, 2, 3,4, 5, 6, 7, 8, 9, 10). Within a maturity group are sub-groups. Asub-group is a tenth of a relative maturity group (for example 1.3 wouldindicate a group 1 and subgroup 3). Within narrow comparisons, thedifference of a tenth of a relative maturity group equates very roughlyto a day difference in maturity at harvest.

PRT or PHYTOPHTHORA FIELD TOLERANCE. Tolerance to Phytophthora root rotis rated on a scale of 1 to 9, with a score of 1 indicating the plantshave no tolerance to Phytophthora, ranging to a score of 9 being thebest or highest tolerance. PRTLAB indicates the tolerance was scoredusing plants in lab assay experiments. Preliminary scores are reportedas double digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

PHYTOPHTHORA RESISTANCE GENE (Rps). Various Phytophthora resistancegenes are known and include, but are not limited to: Rps1-a=resistanceto races 1-2, 10-11, 13-18, 24; Rps1-c=resistance to races 1-3, 6-11,13, 15, 17, 21, 23, 24, 26, 28-30, 32, 34, 36; Rps1-k=resistance toraces 1-11, 13-15, 17, 18, 21-24, 26, 36, 37; Rps3-a=resistance to races1-5, 8, 9, 11, 13, 14, 16, 18, 23, 25, 28, 29, 31-35, 39-41, 43-45,47-52, 54; Rps3-c=resistance to races 1-4, 10-16, 18-36, 38-54;Rps6=resistance to races 1-4, 10, 12, 14-16, 18-21, 25, 28, 33-35; and,Rps8=resistance to races 1-5, 9, 13-15, 21, 25, 29, 32. As reported inthe tables “−” or “ ” indicates that a specific gene for resistance hasnot been identified to date.

PRO=PROTN=PROTN (%)=% Protein=PROTEIN PERCENT. Soybean seeds contain aconsiderable amount of protein. Protein is generally measured by NIRspectrophotometry, and is reported as a percent on a dry weight basis ofthe seed. The percent protein can be measured at a specified moisturecontent of the seed, such as 13% moisture (H₂O).

PUBESCENCE. This refers to a covering of very fine hairs closelyarranged on the leaves, stems and pods of the soybean plant. Pubescencecolor data values include: L=Light Tawny; T=Tawny; G=Gray.

R160=Palmitic Acid percentage. Percentage of palmitic acid as determinedusing methods described in Reske et al. (1997) “TriacylglycerolComposition and Structure in Genetically Modified Sunflower and SoybeanOils” JAOCS 74:989-998, which is incorporated by reference for thispurpose.

R180=Stearic acid percentage. Percentage of Stearic acid as determinedusing methods described in Reske et al. (1997) JAOCS 74:989-998, whichis incorporated by reference for this purpose.

R181=Oleic acid percentage. Percentage of oleic acid as determined usingmethods described in Reske et al. (1997) JAOCS 74:989-998, which isincorporated by reference for this purpose.

R182=Linoleic acid percentage. Percentage of linoleic acid as determinedusing methods described in Reske et al. (1997) JAOCS 74:989-998, whichis incorporated by reference for this purpose.

R183=Linolenic acid percentage. Percentage of linolenic acid asdetermined using methods described in Reske et al. (1997) JAOCS74:989-998, which is incorporated by reference for this purpose.

RESISTANCE. As used herein, resistance is synonymous with tolerance andis used to describe the ability of a plant to withstand exposure to aninsect, disease, herbicide, environmental stress, or other condition. Aresistant plant variety will be able to better withstand the insect,disease pathogen, herbicide, environmental stress, or other condition ascompared to a non-resistant or wild-type variety.

RKI=SOUTHERN ROOT-KNOT NEMATODE. Southern root knot nematode,Meloidogyne incognita, is a plant parasite that can cause major damageto roots, reducing yield potential. Severity is visually scored on rootsin a range from 1 to 9 comparing all genotypes in a given experiment toknown resistant and susceptible checks. The score is determined byvisually scoring the roots for presence or absence of galling in acontrolled chamber bioassay. A score of 1 indicates severe galling ofthe root system which can cause premature death from decomposition ofthe root system (susceptible). A score of 9 indicates that there islittle to no galling of the roots (resistant). Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

RKA=PEANUT ROOT-KNOT NEMATODE. Peanut root knot nematode, Meloidogynearenaria, is a plant parasite that can cause major damage to roots,reducing yield potential. Severity is visually scored on roots in arange from 1 to 9 comparing all genotypes in a given experiment to knownresistant and susceptible checks. The score is determined by visuallyscoring the roots for presence or absence of galling in a controlledchamber bioassay. A score of 1 indicates severe galling of the rootsystem which can cause pre-mature death from decomposition of the rootsystem (susceptible). A score of 9 indicates that there is little to nogalling of the roots (resistant). Preliminary scores are reported asdouble digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

RKJ=JAVANICA ROOT-KNOT NEMATODE. Javanica root knot nematode,Meloidogyne javanica, is a plant parasite that can cause major damage toroots, reducing yield potential. Severity is visually scored on roots ina range from 1 to 9 comparing all genotypes in a given experiment toknown resistant and susceptible checks. The score is determined byvisually scoring the roots for presence or absence of galling in acontrolled chamber bioassay. A score of 1 indicates severe galling ofthe root system which can cause premature death from decomposition ofthe root system (susceptible). A score of 9 indicates that there islittle to no galling of the roots (resistant). Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

SCN=SOYBEAN CYST NEMATODE RESISTANCE=Cyst Nematode Resistance=CystNematode. The score is based on resistance to a particular race ofsoybean cyst nematode (Heterodera glycines), such as race 1, 2, 3, 5 or14 to reproduce on the roots of a plant. Scores are from 1 to 9 andindicate visual observations of the number of female SCN nematodes ascompared to known susceptible genotypes in the test. A score of 1indicates the number of female SCN nematodes is greater than 71% of thenumber observed on known susceptible varieties and cause yield loss,while a score of 9 indicates the number of female SCN nematodes is lessthan 7% of the number observed on known susceptible varieties, and theline shows strong SCN resistance. Preliminary scores are reported asdouble digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

SCN Resistance Source. There are three typical sources of geneticresistance to SCN: PI88788, PI548402 (also known as Peking), andPI437654.

SCN infected soils. Soils containing soybean cyst nematode.

SD VIG or Seedling Vigor. The score is based on the speed of emergenceof the plants within a plot relative to other plots within anexperiment.

A score of 1 indicates no plants have expanded first leaves, while ascore of 9 indicates that 90% of plants growing have expanded firstleaves.

SDS or SUDDEN DEATH SYNDROME. SDS is caused by the fungal pathogenformerly known as Fusarium solani f.sp. glycines, which is currentlyknown as Fusarium virguliforme (see, e.g., Aoki et al. (2003) Mycologia95:660-684). Tolerance to Sudden Death Syndrome is rated on a scale of 1to 9, with a score of 1 being very susceptible ranging up to a score of9 being tolerant. Preliminary scores are reported as double digits, forexample ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

SEED COAT LUSTER. Data values include D=dull; S=shiny.

SEED PROTEIN PEROXIDASE ACTIVITY. Varieties can be classified as high,low, or mixed for peroxidase activity and is scored as H=high, L=low,M=mixed. If mixed value, the percentage of high and low seeds can becalculated. For example: a variety mixed for peroxidase may have 40% ofseeds high and 60% of seeds low for peroxidase activity.

SEED SHAPE. Soybean seed shapes are measured using calipers. Shapes canbe SP=spherical, SPF=spherical flattened, E=elongate, or EF=elongateflattened.

SEED SIZE SCORE. This is a measure of the seed size from 1 to 9. Thehigher the score, the smaller the seed size measured. Preliminary scoresare reported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

SEPTORIA LEAF SPOT. Septoria Leaf Spot, also known as Brown Spot, iscaused by the fungus Septoria glycines. Symptoms can occur as early asV2 on lower leaves, and may move up the plant affecting leaves as wellas stems and pods in plants approaching maturity. Symptoms includeirregular dark brown spots on upper and lower leaf surfaces, or thestems or pods. Infected leaves may yellow or brown and drop early.Tolerance to Septoria Leaf Spot is rated on a scale of 1 to 9, with ascore of 1 being very susceptible ranging up to a score of 9 beingtolerant. Preliminary scores are reported as double digits, for example‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

SHATTR or Shattering. This refers to the amount of pod dehiscence priorto harvest. Pod dehiscence involves seeds falling from the pods to thesoil. This is a visual score from 1 to 9 comparing all genotypes withina given test. A score of 1 indicates 100% of the pods are opened, whilea score of 9 means pods have not opened and no seeds have fallen out.

SHOOTS. These are a portion of the body of the plant. They consist ofstems, petioles and leaves.

SOYBEAN MOSAIC VIRUS or SMV. Soybean mosaic virus (SMV) is a pathogenicplant virus which belongs to the Potyviridae family and believed to bespread by aphids. Viral infection in soybean can cause stunting ofplants as well as crinkling and mottling of leaves. Leaf blades can bepuckered along the veins and curled downward. Mottling appears as lightand dark green patches on leaves. SMV can also reduce seed size and/orpod number per plant, as well as contributing to seed discolorationassociated with the hilum. Tolerance to SMV is rated visually on a scaleof 1 to 9, with a score of 1 being very susceptible ranging up to ascore of 9 being tolerant. Preliminary scores are reported as doubledigits, for example ‘55’ indicates a preliminary score of 5 on the scaleof 1 to 9.

SPLB=S/LB=Seeds per Pound. Soybean seeds vary in seed size, therefore,the number of seeds required to make up one pound also varies. Thisaffects the pounds of seed required to plant a given area, and can alsoimpact end uses.

STC or Stearic Acid Percent. Stearic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

STRESS ENVIRONMENTS. Areas which have one or more conditions that do notpermit the full expression of high yield. These conditions may be causedby biotic or abiotic stresses.

SUBLINE. Although XB39Q15R contains substantially fixed genetics, and isphenotypically uniform and with no off-types expected, there stillremains a small proportion of segregating loci either within individualsor within the population as a whole. The segregating loci both withinany individual plant and/or the population can be used to extract uniquevarieties (sublines) with similar phenotype but improved agronomics.

TARGET SPOT. This is a fungal disease caused by Corynespora cassiicola.Symptoms usually consist of roughly circular, necrotic leaf lesionsranging in size from minute to 11 mm in diameter, though typicallyapproximately 4 to 5 mm in diameter, and with a yellow margin. Largelesions occasionally exhibit a zonate pattern associated with thisdisease. Tolerance to target spot is scored from 1 to 9 by visuallycomparing all genotypes in a given test. A score of 1 indicates completedeath of the experimental unit while a score of 9 indicates no symptoms.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

WHMD or WHITE MOLD TOLERANCE=WHITE MOLD. This is a fungal disease causedby Sclerotinia sclerotiorum that creates mycelial growth and death ofplants. Tolerance to white mold is scored from 1 to 9 by visuallycomparing all genotypes in a given test. A score of 1 indicates completedeath of the experimental unit while a score of 9 indicates no symptoms.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

VARIETY. A substantially homozygous soybean line and minor modificationsthereof that retains the overall genetics of the soybean line includingbut not limited to a subline, a locus conversion, a mutation, atransgenic, or a somaclonal variant. Variety includes seeds, plants,plant parts, and/or seed parts of the instant soybean line.

YIELD. Unless stated to the contrary, yield values are given in bushelsper acre (bu/a) at 13% moisture.

Soybean Variety XB39Q15R

Soybean variety XB39Q15R has shown uniformity and stability for alltraits, as described in the following variety description information.Soybean variety XB39Q15R was developed from a cross of variety RJS40001with variety 93Y82. Variety XB39Q15R is an F3-derived line which wasadvanced to the F3 generation by modified single seed descent. It hasbeen self-pollinated a sufficient number of generations, with carefulattention to uniformity of plant type to ensure a sufficient level ofhomozygosity and phenotypic stability. The variety has been increasedwith continued observation for uniformity. No variant traits have beenobserved or are expected.

A variety description of soybean variety XB39Q15R is provided inTable 1. Traits reported are average values for all locations and yearsor samples measured. Preliminary scores are reported as double digits,for example ‘55’ indicates a preliminary score of 5 on the scale of 1 to9.

Table 2 shows the BLUP (Best Linear Unbiased Prediction) values for arange of traits and characteristics of soybean variety XB39Q15Rdetermined from a mixed model analysis of variety performanceobservations taken from plants grown at various locations andreplications.

Soybean variety XB39Q15R, being substantially homozygous, can bereproduced by planting seeds of the variety, growing the resultingsoybean plants under self-pollinating or sib-pollinating conditions, andharvesting the resulting seed, using techniques familiar to theagricultural arts. Development of soybean variety XB39Q15R is shown inthe breeding history summary in Table 3.

Genetic Marker Profile

In addition to phenotypic observations, a plant can also be identifiedby its genotype. The genotype of a plant can be characterized through agenetic marker profile which can identify plants of the same variety ora related variety, or which can be used to determine or validate apedigree. Genetic marker profiles can be obtained by techniques such asrestriction fragment length polymorphisms (RFLPs), randomly amplifiedpolymorphic DNAs (RAPDs), arbitrarily primed polymerase chain reaction(AP-PCR), DNA amplification fingerprinting (DAF), sequence characterizedamplified regions (SCARs), amplified fragment length polymorphisms(AFLPs), simple sequence repeats (SSRs) also referred to asmicrosatellites, single nucleotide polymorphisms (SNPs), or genome-wideevaluations such as genotyping-by-sequencing (GBS). For example, seeCregan et al. (1999) “An Integrated Genetic Linkage Map of the SoybeanGenome” Crop Science 39:1464-1490, and Berry et al. (2003) “AssessingProbability of Ancestry Using Simple Sequence Repeat Profiles:Applications to Maize Inbred Lines and Soybean Varieties” Genetics165:331-342, each of which are incorporated by reference herein in theirentirety. Favorable genotypes and or marker profiles, optionallyassociated with a trait of interest, may be identified by one or moremethodologies. In some examples one or more markers are used, includingbut not limited to AFLPs, RFLPs, ASH, SSRs, SNPs, indels, padlockprobes, molecular inversion probes, microarrays, sequencing, and thelike. In some methods, a target nucleic acid is amplified prior tohybridization with a probe. In other cases, the target nucleic acid isnot amplified prior to hybridization, such as methods using molecularinversion probes (see, for example Hardenbol et al. (2003) Nat Biotech21:673-678). In some examples, the genotype related to a specific traitis monitored, while in other examples, a genome-wide evaluationincluding but not limited to one or more of marker panels, libraryscreens, association studies, microarrays, gene chips, expressionstudies, or sequencing such as whole-genome resequencing andgenotyping-by-sequencing (GBS) may be used. In some examples, notarget-specific probe is needed, for example by using sequencingtechnologies, including but not limited to next-generation sequencingmethods (see, for example, Metzker (2010) Nat Rev Genet 11:31-46; and,Egan et al. (2012) Am J Bot 99:175-185) such as sequencing by synthesis(e.g., Roche 454 pyrosequencing, Illumina Genome Analyzer, and IonTorrent PGM or Proton systems), sequencing by ligation (e.g., SOLiD fromApplied Biosystems, and Polnator system from Azco Biotech), and singlemolecule sequencing (SMS or third-generation sequencing) which eliminatetemplate amplification (e.g., Helicos system, and PacBio RS system fromPacific BioSciences). Further technologies include optical sequencingsystems (e.g., Starlight from Life Technologies), and nanoporesequencing (e.g., GridION from Oxford Nanopore Technologies). Each ofthese may be coupled with one or more enrichment strategies fororganellar or nuclear genomes in order to reduce the complexity of thegenome under investigation via PCR, hybridization, restriction enzyme(see, e.g., Elshire et al. (2011) PLoS ONE 6:e19379), and expressionmethods. In some examples, no reference genome sequence is needed inorder to complete the analysis.

Methods are provided of characterizing soybean variety XB39Q15R, or avariety comprising the phenotypic characteristics, morphologicalcharacteristics, physiological characteristics or combination thereof ofsoybean variety XB39Q15R. A method comprising isolating nucleic acids,such as DNA, from a plant, a plant part, plant cell or a seed of thesoybean variety disclosed herein is provided. The method can includemechanical, electrical and/or chemical disruption of the plant, plantpart, plant cell or seed, contacting the disrupted plant, plant part,plant cell or seed with a buffer or solvent, to produce a solution orsuspension comprising nucleic acids, optionally contacting the nucleicacids with a precipiting agent to precipitate the nucleic acids,optionally extracting the nucleic acids, and optionally separating thenucleic acids such as by centrifugation or by binding to beads or acolumn, with subsequent elution, or a combination thereof. If DNA isbeing isolated, an RNase can be included in one or more of the methodsteps. The nucleic acids isolated can comprise all or substantially allof the genomic DNA sequence, all or substantially all of the chromosomalDNA sequence or all or substantially all of the coding sequences (cDNA)of the plant, plant part, or plant cell from which they were isolated.The amount and type of nucleic acids isolated may be sufficient topermit whole genome sequencing of the plant from which they wereisolated or chromosomal marker analysis of the plant from which theywere isolated.

The methods can be used to produce nucleic acids from the plant, plantpart, seed or cell, which nucleic acids can be, for example, analyzed toproduce data. The data can be recorded. The nucleic acids from thedisrupted cell, the disrupted plant, plant part, plant cell or seed orthe nucleic acids following isolation or separation can be contactedwith primers and nucleotide bases, and/or a polymerase to facilitate PCRsequencing or marker analysis of the nucleic acids. In some examples,the nucleic acids produced can be sequenced or contacted with markers toproduce a genetic profile, a molecular profile, a marker profile, ahaplotype, or any combination thereof. In some examples, the geneticprofile or nucleotide sequence is recorded on a computer readablemedium. In other examples, the methods may further comprise using thenucleic acids produced from plants, plant parts, plant cells or seeds ina plant breeding program, for example in making soybean crossing,selection and/or advancement decisions in a breeding program. Crossingincludes any type of plant breeding crossing method, including but notlimited to outcrossing, selfing, backcrossing, locus conversion,introgression and the like.

In some examples, one or more markers are used to characterize and/orevaluate a soybean variety. Particular markers used for these purposesare not limited to any particular set of markers, but are envisioned toinclude any type of marker and marker profile which provides a means ofdistinguishing varieties. For example, one method of comparison is touse only homozygous loci for XB39Q15R.

Primers and PCR protocols for assaying these and other markers aredisclosed in Soybase (sponsored by the USDA Agricultural ResearchService and Iowa State University) which is available online. Inaddition to being used for identification of soybean variety XB39Q15Rand plant parts and plant cells of variety XB39Q15R, the genetic profilemay be used to identify a soybean plant produced through the use ofXB39Q15R or to verify a pedigree for progeny plants produced through theuse of XB39Q15R. The genetic marker profile is also useful in breedingand developing backcross conversions.

The present invention comprises a soybean plant characterized bymolecular and physiological data obtained from the representative sampleof said variety deposited with the American Type Culture Collection(ATCC). Thus, plants, seeds, or parts thereof, having all orsubstantially all of the physiological, morphological, and/or phenotypiccharacteristics of soybean variety XB39Q15R are provided. Furtherprovided is a soybean plant formed by the combination of the disclosedsoybean plant or plant cell with another soybean plant or cell andcomprising the homozygous alleles of the variety. A soybean plantcomprising all of the physiological, morphological and/or phenotypiccharacteristics of soybean variety XB39Q15R can be combined with anothersoybean plant in a soybean breeding program. In some examples the othersoybean plant comprises all of the physiological, morphological and/orphenotypic characteristics of soybean variety XB39Q15R.

In some examples, a plant, a plant part, or a seed of soybean varietyXB39Q15R is characterized by producing a molecular profile. A molecularprofile includes but is not limited to one or more genotypic and/orphenotypic profile(s). A genotypic profile includes but is not limitedto a marker profile, such as a genetic map, a linkage map, a traitmarker profile, a SNP profile, an SSR profile, a genome-wide markerprofile, a haplotype, and the like. A molecular profile may also be anucleic acid sequence profile, and/or a physical map. A phenotypicprofile includes but is not limited to one or more phenotypic traits, aprotein expression profile, a metabolic profile, an mRNA expressionprofile, and the like.

Means of performing genetic marker profiles using SSR polymorphisms arewell known in the art. A marker system based on SSRs can be highlyinformative in linkage analysis relative to other marker systems in thatmultiple alleles may be present. Another advantage of this type ofmarker is that, through use of flanking primers, detection of SSRs canbe achieved, for example, by using the polymerase chain reaction (PCR),thereby eliminating the need for labor-intensive Southern hybridization.PCR detection is done using two oligonucleotide primers flanking thepolymorphic segment of repetitive DNA to amplify the SSR region.

Following amplification, markers can be scored by electrophoresis of theamplification products. Scoring of marker genotype is based on the sizeof the amplified fragment, which correlates to the number of base pairsof the fragment. While variation in the primer used or in laboratoryprocedures can affect the reported fragment size, relative values shouldremain constant regardless of the specific primer or laboratory used.When comparing varieties it is preferable if all SSR profiles areperformed in the same lab.

Primers used are publicly available and may be found in the Soybasedatabase or Unigene database (each available online), Cregan (1999 CropScience 39:1464-1490), Choi et al. (2007 Genetics 176:685-696), andHyten et al. (2010 Crop Sci 50:960-968). See also, WO 99/31964“Nucleotide Polymorphisms in Soybean”, U.S. Pat. No. 6,162,967“Positional Cloning of Soybean Cyst Nematode Resistance Genes”, and U.S.Pat. No. 7,288,386 “Soybean Sudden Death Syndrome Resistant Soybeans andMethods of Breeding and Identifying Resistant Plants”, the disclosuresof which are incorporated herein by reference.

The SSR profile of soybean plant XB39Q15R can be used to identify plantscomprising XB39Q15R as a parent, since such plants will comprise thesame homozygous alleles as XB39Q15R. Because the soybean variety isessentially homozygous at all relevant loci, most loci should have onlyone type of allele present. In contrast, a genetic marker profile of anF1 progeny should be the sum of those parents, e.g., if one parent washomozygous for allele X at a particular locus, and the other parenthomozygous for allele Y at that locus, then the F1 progeny will be XY(heterozygous) at that locus. Subsequent generations of progeny producedby selection and breeding are expected to be of genotype XX(homozygous), YY (homozygous), or XY (heterozygous) for that locusposition. When the F1 plant is selfed or sibbed for successive filialgenerations, the locus should be either X or Y for that position.

In addition, plants and plant parts substantially benefiting from theuse of XB39Q15R in their development, such as XB39Q15R comprising abackcross conversion, transgene, or genetic sterility factor, may beidentified by having a molecular marker profile with a high percentidentity to XB39Q15R. Such a percent identity might be 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 99.9% identical toXB39Q15R.

The SSR profile of variety XB39Q15R also can be used to identifyessentially derived varieties and other progeny varieties developed fromthe use of XB39Q15R, as well as cells and other plant parts thereof.Plants of the invention include any plant having at least 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 99.9% of the markers in theSSR profile, and that retain 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, 99%, 99.5%, or 99.9% of the physiological and morphologicalcharacteristics of variety XB39Q15R when grown under the sameconditions. Such plants may be developed using the markers identified inWO00/31964, U.S. Pat. No. 6,162,967 and U.S. Pat. No. 7,288,386. Progenyplants and plant parts produced using XB39Q15R may be identified byhaving a molecular marker profile of at least 25%, 30%, 35%, 40%, 45%,50%, 55%, 60%, 65%, 70%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%,84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, 99% or 99.5% genetic contribution from soybean variety XB39Q15R, asmeasured by either percent identity or percent similarity. Such progenymay be further characterized as being within a pedigree distance ofXB39Q15R, such as within 1, 2, 3, 4, or 5 or less cross-pollinations toa soybean plant other than XB39Q15R, or a plant that has XB39Q15R as aprogenitor. Unique molecular profiles may be identified with othermolecular tools such as SNPs and RFLPs.

Introduction of a New Trait or Locus into XB39Q15R

Variety XB39Q15R represents a new base genetic variety into which a newlocus or trait may be introduced or introgressed. Transformation andbackcrossing represent two methods that can be used to accomplish suchan introgression.

A backcross conversion of XB39Q15R occurs when DNA sequences areintroduced through backcrossing (Hallauer et al. in Corn and CornImprovement, Sprague and Dudley, Third Ed. 1998) with XB39Q15R utilizedas the recurrent parent. Both naturally occurring and transgenic DNAsequences may be introduced through backcrossing techniques. A backcrossconversion may produce a plant with a trait or locus conversion in atleast two or more backcrosses, including at least 2 backcrosses, atleast 3 backcrosses, at least 4 backcrosses, at least 5 backcrosses, atleast 6 backcrosses or more, depending at least in part on thedifferences between the parents of the original cross. Molecular markerassisted breeding or selection may be utilized to reduce the number ofbackcrosses necessary to achieve the backcross conversion. For example,see Openshaw et al., “Marker-assisted Selection in Backcross Breeding,”In: Proceedings Symposium of the Analysis of Molecular Data, August1994, Crop Science Society of America, Corvallis, Oreg., whichdemonstrated that a backcross conversion can be made in as few as twobackcrosses.

The complexity of the backcross conversion method depends on the type oftrait being transferred (a single gene or closely linked genes comparedto unlinked genes), the level of expression of the trait, the type ofinheritance (cytoplasmic or nuclear), dominant or recessive traitexpression, and the types of parents included in the cross. It isunderstood by those of ordinary skill in the art that for single genetraits that are relatively easy to classify, the backcross method iseffective and relatively easy to manage. (See Hallauer et al., in Cornand Corn Improvement, Sprague and Dudley, Third Ed. 1998). Desiredtraits that may be transferred through backcross conversion include, butare not limited to, sterility (nuclear and cytoplasmic), fertilityrestoration, nutritional enhancements, drought tolerance, nitrogenutilization, altered fatty acid profile, low phytate, industrialenhancements, disease resistance (bacterial, fungal, or viral), insectresistance, and herbicide resistance. In addition, a recombination siteitself, such as an FRT site, Lox site, or other site specificintegration site, may be inserted by backcrossing and utilized fordirect insertion of one or more genes of interest into a specific plantvariety. A single locus may contain several transgenes, such as atransgene for disease resistance and a transgene for herbicideresistance. The gene for herbicide resistance may be used as aselectable marker and/or as a phenotypic trait. A single locusconversion of site specific integration system allows for theintegration of multiple genes at a known recombination site in thegenome. At least one, at least two or at least three and less than ten,less than nine, less than eight, less than seven, less than six, lessthan five or less than four locus conversions may be introduced into theplant by backcrossing, introgression or transformation to express thedesired trait, while the plant, or a plant grown from the seed, plantpart or plant cell, otherwise retains the phenotypic characteristics ofthe deposited seed when grown under the same environmental conditions.

The backcross conversion may result from either the transfer of adominant allele or a recessive allele. Selection of progeny containingthe trait of interest can be accomplished by direct selection for atrait associated with a dominant allele. Transgenes transferred viabackcrossing typically function as a dominant single gene trait and arerelatively easy to classify. Selection of progeny for a trait that istransferred via a recessive allele requires growing and selfing thefirst backcross generation to determine which plants carry the recessivealleles. Recessive traits may require additional progeny testing insuccessive backcross generations to determine the presence of the locusof interest. The last backcross generation is usually selfed to givepure breeding progeny for the trait(s) being transferred, although abackcross conversion with a stably introgressed trait may also bemaintained by further backcrossing to the recurrent parent withsubsequent selection for the trait.

Along with selection for the trait of interest, progeny are selected forthe phenotype of the recurrent parent. The backcross is a form ofinbreeding, and the features of the recurrent parent are automaticallyrecovered after successive backcrosses. Poehlman suggests from one tofour or more backcrosses, but as noted above, the number of backcrossesnecessary can be reduced with the use of molecular markers (Poehlman etal. (1995) Breeding Field Crops, 4th Ed., Iowa State University Press,Ames, Iowa). Other factors, such as a genetically similar donor parent,may also reduce the number of backcrosses necessary. As noted byPoehlman, backcrossing is easiest for simply inherited, dominant, andeasily recognized traits.

One process for adding or modifying a trait or locus in soybean varietyXB39Q15R comprises crossing XB39Q15R plants grown from XB39Q15R seedwith plants of another soybean variety that comprises a desired traitlacking in XB39Q15R, selecting F1 progeny plants that possess thedesired trait or locus to produce selected F1 progeny plants, crossingthe selected progeny plants back to XB39Q15R plants to producebackcross1 (BC1) progeny plants. The BC1F1 progeny plants that have thedesired trait and the morphological characteristics of soybean varietyXB39Q15R are selected and backcrossed to XB39Q15R to generate BC2F1progeny plants. Additional backcrossing and selection of progeny plantswith the desired trait will produce BC3F1, BC4F1, BC5F1, . . . BCxF1generations of plants. The backcross populations of XB39Q15R may befurther characterized as having the phenotypic, physiological and/ormorphological characteristics of soybean variety XB39Q15R, such aslisted in Table 1 and/or Table 2, as determined at the 5% significancelevel when grown in the same environmental conditions and/or may becharacterized by percent similarity or identity to XB39Q15R asdetermined by SSR or other molecular markers. The above method may beutilized with fewer backcrosses in appropriate situations, such as whenthe donor parent is highly related or molecular markers are used in oneor more selection steps. Desired traits that may be used include thosenucleic acids known in the art, some of which are listed herein, thatwill affect traits through nucleic acid expression or inhibition.Desired loci also include the introgression of FRT, Lox, and/or otherrecombination sites for site specific integration. Desired loci furtherinclude QTLs, which may also affect a desired trait.

In addition, the above process and other similar processes describedherein may be used to produce first generation progeny soybean seed byadding a step at the end of the process that comprises crossing XB39Q15Rwith the introgressed trait or locus with a different soybean plant andharvesting the resultant first generation progeny soybean seed.

Transgenes and transformation methods provide means to engineer thegenome of plants to contain and express heterologous genetic elements,including but not limited to foreign genetic elements, additional copiesof endogenous elements, and/or modified versions of native or endogenousgenetic elements, in order to alter at least one trait of a plant in aspecific manner. Any heterologous DNA sequence(s), whether from adifferent species or from the same species, which are inserted into thegenome using transformation, backcrossing, or other methods known to oneof skill in the art are referred to herein collectively as transgenes.The sequences are heterologous based on sequence source, location ofintegration, operably linked elements, or any combination thereof. Oneor more transgenes of interest can be introduced into soybean varietyXB39Q15R. Transgenic variants of soybean variety XB39Q15R plants, seeds,cells, and parts thereof or derived therefrom are provided. Transgenicvariants of XB39Q15R comprise the physiological and morphologicalcharacteristics of soybean variety XB39Q15R, such as listed in Table 1as determined at the 5% significance level when grown in the sameenvironmental conditions, and/or may be characterized or identified bypercent similarity or identity to XB39Q15R as determined by SSR or othermolecular markers. In some examples, transgenic variants of soybeanvariety XB39Q15R are produced by introducing at least one transgene ofinterest into soybean variety XB39Q15R by transforming XB39Q15R with apolynucleotide comprising the transgene of interest. In other examples,transgenic variants of soybean variety XB39Q15R are produced byintroducing at least one transgene by introgressing the transgene intosoybean variety XB39Q15R by crossing.

In one example, a process for modifying soybean variety XB39Q15R withthe addition of a desired trait, said process comprising transforming asoybean plant of variety XB39Q15R with a transgene that confers adesired trait is provided. Therefore, transgenic XB39Q15R soybean cells,plants, plant parts, and seeds produced from this process are provided.In some examples one more desired traits may include traits such asherbicide resistance, insect resistance, disease resistance, decreasedphytate, modified fatty acid profile, modified fatty acid content,carbohydrate metabolism, protein content, or oil content. The specificgene may be any known in the art or listed herein, including but notlimited to a polynucleotide conferring resistance to an ALS-inhibitorherbicide, imidazolinone, sulfonylurea, protoporphyrinogen oxidase (PPO)inhibitors, hydroxyphenyl pyruvate dioxygenase (HPPD) inhibitors,glyphosate, glufosinate, triazine, 2,4-dichlorophenoxyacetic acid(2,4-D), dicamba, broxynil, metribuzin, or benzonitrile herbicides; apolynucleotide encoding a Bacillus thuringiensis polypeptide, apolynucleotide encoding a phytase, a fatty acid desaturase (e.g., FAD-2,FAD-3), galactinol synthase, a raffinose synthetic enzyme; or apolynucleotide conferring resistance to soybean cyst nematode, brownstem rot, Phytophthora root rot, soybean mosaic virus, sudden deathsyndrome, or other plant pathogen.

Numerous methods for plant transformation have been developed, includingbiological and physical plant transformation protocols. See, forexample, Miki et al., “Procedures for Introducing Foreign DNA intoPlants” in Methods in Plant Molecular Biology and Biotechnology, Glick,B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages67-88; and Armstrong (1999) “The First Decade of Maize Transformation: AReview and Future Perspective” Maydica 44:101-109. In addition,expression vectors and in vitro culture methods for plant cell or tissuetransformation and regeneration of plants are available. See, forexample, Gruber et al., “Vectors for Plant Transformation” in Methods inPlant Molecular Biology and Biotechnology, Glick, B. R. and Thompson, J.E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages 89-119.

In general, methods to transform, modify, edit or alter plant endogenousgenomic DNA include altering the plant native DNA sequence or apre-existing transgenic sequence including regulatory elements, codingand non-coding sequences. These methods can be used, for example, totarget nucleic acids to pre-engineered target recognition sequences inthe genome. Such pre-engineered target sequences may be introduced bygenome editing or modification. As an example, a genetically modifiedplant variety is generated using “custom” or engineered endonucleasessuch as meganucleases produced to modify plant genomes (see e.g., WO2009/114321; Gao et al. (2010) Plant Journal 1:176-187). Anothersite-directed engineering method is through the use of zinc fingerdomain recognition coupled with the restriction properties ofrestriction enzyme. See e.g., Urnov, et al., (2010) Nat Rev Genet.11(9):636-46; Shukla, et al., (2009) Nature 459 (7245):437-41. Atranscription activator-like (TAL) effector-DNA modifying enzyme (TALEor TALEN) is also used to engineer changes in plant genome. See e.g.,US20110145940, Cermak et al., (2011) Nucleic Acids Res. 39(12) and Bochet al., (2009), Science 326(5959): 1509-12. Site-specific modificationof plant genomes can also be performed using the bacterial type IICRISPR (clustered regularly interspaced short palindromic repeats)/Cas(CRISPR-associated) system. See e.g., Belhaj et al., (2013), PlantMethods 9: 39; The Cas9/guide RNA-based system allows targeted cleavageof genomic DNA guided by a customizable small noncoding RNA in plants(see e.g., WO 2015026883A1, incorporated herein by reference).

Plant transformation methods may involve the construction of anexpression vector. Such a vector or recombinant construct comprises aDNA sequence that contains a coding sequence, such as a protein and/orRNA coding sequence under the control of or operatively linked to aregulatory element, for example a promoter. The vector or construct maycontain one or more coding sequences and one or more regulatoryelements.

A genetic trait which has been engineered into the genome of aparticular soybean plant may then be moved into the genome of anothervariety using traditional breeding techniques that are well known in theplant breeding arts. For example, a backcrossing approach is commonlyused to move a transgene from a transformed soybean variety into anelite soybean variety, and the resulting backcross conversion plantwould then contain the transgene(s).

Various genetic elements can be introduced into the plant genome usingtransformation. These elements include, but are not limited to genes;coding sequences; inducible, constitutive, and tissue specificpromoters; enhancing sequences; and signal and targeting sequences.

A genetic map can be generated that identifies the approximatechromosomal location of the integrated DNA molecule, for example viaconventional restriction fragment length polymorphisms (RFLP),polymerase chain reaction (PCR) analysis, simple sequence repeats (SSR),and single nucleotide polymorphisms (SNP). For exemplary methodologiesin this regard, see Glick and Thompson, Methods in Plant MolecularBiology and Biotechnology, pp. 269-284 (CRC Press, Boca Raton, 1993).

Wang et al. discuss “Large Scale Identification, Mapping and Genotypingof Single-Nucleotide Polymorphisms in the Human Genome”, Science (1998)280:1077-1082, and similar capabilities are increasingly available forthe soybean genome. Map information concerning chromosomal location isuseful for proprietary protection of a subject transgenic plant. Ifunauthorized propagation is undertaken and crosses made with othergermplasm, the map of the integration region can be compared to similarmaps for suspect plants to determine if the latter have a commonparentage with the subject plant. Map comparisons could involvehybridizations, RFLP, PCR, SSR, sequencing or combinations thereof, allof which are conventional techniques. SNPs may also be used alone or incombination with other techniques.

Likewise, plants can be genetically engineered to express variousphenotypes of agronomic interest. Through the transformation of soybeanthe expression of genes can be altered to enhance disease resistance,insect resistance, herbicide resistance, agronomic, grain quality, andother traits. Transformation can also be used to insert DNA sequenceswhich control or help control male-sterility. DNA sequences native tosoybean as well as non-native DNA sequences can be transformed intosoybean and used to alter levels of native or non-native proteins.Various promoters, targeting sequences, enhancing sequences, and otherDNA sequences can be inserted into the genome for the purpose ofaltering the expression of proteins. Reduction of the activity ofspecific genes (also known as gene silencing or gene suppression) isdesirable for several aspects of genetic engineering in plants.

Many techniques for gene silencing are well known to one of skill in theart, including but not limited to, knock-outs (such as by insertion of atransposable element such as mu (Vicki Chandler, The Maize Handbook Ch.118 (Springer-Verlag 1994)); antisense technology (see, e.g., Sheehy etal. (1988) PNAS USA 85:8805-8809; and U.S. Pat. Nos. 5,107,065;5,453,566; and 5,759,829); co-suppression (e.g., Taylor (1997) PlantCell 9:1245; Jorgensen (1990) Trends Biotech 8:340-344; Flavell (1994)PNAS USA 91:3490-3496; Finnegan et al. (1994) Bio/Technology 12:883-888;and Neuhuber et al. (1994) Mol Gen Genet 244:230-241); RNA interference(Napoli et al. (1990) Plant Cell 2:279-289; U.S. Pat. No. 5,034,323;Sharp (1999) Genes Dev 13:139-141; Zamore et al. (2000) Cell 101:25-33;and Montgomery et al. (1998) PNAS USA 95:15502-15507); virus-inducedgene silencing (Burton et al. (2000) Plant Cell 12:691-705; Baulcombe(1999) Curr Op Plant Biol 2:109-113); target-RNA-specific ribozymes(Haseloff et al. (1988) Nature 334: 585-591); hairpin structures (Smithet al. (2000) Nature 407:319-320; WO99/53050; WO98/53083); microRNA(Aukerman & Sakai (2003) Plant Cell 15:2730-2741); ribozymes (Steineckeet al. (1992) EMBO J 11:1525; Perriman et al. (1993) Antisense Res Dev3:253); oligonucleotide mediated targeted modification (e.g.,WO03/076574 and WO99/25853); Zn-finger targeted molecules (e.g.,WO01/52620; WO03/048345; and WO00/42219); use of exogenously applied RNA(e.g., US20110296556); and other methods or combinations of the abovemethods known to those of skill in the art.

Exemplary nucleotide sequences and/or native loci that confer at leastone trait of interest, which optionally may be conferred or altered bygenetic engineering, transformation or introgression of a transformedevent include, but are not limited to, those categorized below.

1. Genes that Confer Resistance to Insects or Disease and that Encode:

(A) Plant disease resistance genes. Plant defenses are often activatedby specific interaction between the product of a disease resistance gene(R) in the plant and the product of a corresponding avirulence (Avr)gene in the pathogen. A plant variety can be transformed with clonedresistance gene to engineer plants that are resistant to specificpathogen strains. A plant resistant to a disease is one that is moreresistant to a pathogen as compared to the wild type plant. See, forexample U.S. Pat. No. 9,169,489, disclosing soybean plants expressing asoybean homolog of glycine-rich protein 7 (GRP7) and providing increasedinnate immunity.

Examples of fungal diseases on leaves, stems, pods and seeds include,for example, Alternaria leaf spot (Alternaria spec. atrans tenuissima),Anthracnose (Colletotrichum gloeosporoides dematium var. truncatum),brown spot (Septoria glycines), cercospora leaf spot and blight(Cercospora kikuchii), choanephora leaf blight (Choanephorainfiindibulifera trispora (Syn.)), dactuliophora leaf spot(Dactuliophora glycines), downy mildew (Peronospora manshurica),drechslera blight (Drechslera glycini), frogeye leaf spot (Cercosporasojina), leptosphaerulina leaf spot (Leptosphaerulina trifolii),phyllostica leaf spot (Phyllosticta sojaecola), pod and stem blight(Phomopsis sojae), powdery mildew (Microsphaera diffusa), pyrenochaetaleaf spot (Pyrenochaeta glycines), rhizoctonia aerial, foliage, and webblight (Rhizoctonia solani), rust (Phakopsora pachyrhizi, Phakopsorameibomiae), scab (Sphaceloma glycines), stemphylium leaf blight(Stemphylium botryosum), target spot (Corynespora cassiicola).

Examples of fungal diseases on roots and the stem base include, forexample, black root rot (Calonectria crotalariae), charcoal rot(Macrophomina phaseolina), fusarium blight or wilt, root rot, and podand collar rot (Fusarium oxysporum, Fusarium orthoceras, Fusariumsemitectum, Fusarium equiseti), mycoleptodiscus root rot(Mycoleptodiscus terrestris), neocosmospora (Neocosmospora vasinfecta),pod and stem blight (Diaporthe phaseolorum), stem canker (Diaporthephaseolorum var. caulivora), phytophthora rot (Phytophthora megasperma),brown stem rot (Phialophora gregata), pythium rot (Pythiumaphanidermatum, Pythium irregulare, Pythium debaryanum, Pythiummyriotylum, Pythium ultimum), rhizoctonia root rot, stem decay, anddamping-off (Rhizoctonia solani), sclerotinia stem decay (Sclerotiniasclerotiorum), sclerotinia southern blight (Sclerotinia rolfsii),thielaviopsis root rot (Thielaviopsis basicola).

(B) A Bacillus thuringiensis (Bt) protein, a derivative thereof or asynthetic polypeptide modeled thereon. Non-limiting examples of Bttransgenes being genetically engineered are given in the followingpatents and patent applications, and hereby are incorporated byreference for this purpose: U.S. Pat. Nos. 5,188,960; 5,689,052;5,880,275; 5,986,177; 7,105,332; 7,208,474; WO91/14778; WO99/31248;WO01/12731; WO99/24581; WO97/40162; US2002/0151709; US2003/0177528;US2005/0138685; US/20070245427; US2007/0245428; US2006/0241042;US2008/0020966; US2008/0020968; US2008/0020967; US2008/0172762;US2008/0172762; and US2009/0005306.

(C) An insect-specific hormone or pheromone such as an ecdysteroid orjuvenile hormone, a variant thereof, a mimetic based thereon, or anantagonist or agonist thereof. (D) An insect-specific peptide which,upon expression, disrupts the physiology of the affected pest.

(E) An enzyme responsible for a hyperaccumulation of a monoterpene, asesquiterpene, a steroid, hydroxamic acid, a phenylpropanoid derivative,or another non-protein molecule with insecticidal activity.

(F) An enzyme involved in the modification, including thepost-translational modification, of a biologically active molecule; forexample, a glycolytic enzyme, a proteolytic enzyme, a lipolytic enzyme,a nuclease, a cyclase, a transaminase, an esterase, a hydrolase, aphosphatase, a kinase, a phosphorylase, a polymerase, an elastase, achitinase and a glucanase, whether natural or synthetic. See, forexample, International Publication WO93/02197, U.S. Pat. Nos. 6,563,020;7,145,060; and 7,087,810 which are herein are incorporated by referencefor this purpose.

(G) A molecule that stimulates signal transduction, such as calmodulin.

(H) A hydrophobic moment peptide, such as peptides based on cecropins(cecropin A or B), magainins, melittin, tachyplesin (see InternationalPublication WO95/16776 and U.S. Pat. No. 5,580,852 disclosing peptidederivatives of tachyplesin which inhibit fungal plant pathogens), andsynthetic antimicrobial peptides that confer disease resistance (see,e.g. International Publication WO95/18855 and U.S. Pat. No. 5,607,914).

(I) A membrane permease, a channel former, or a channel blocker.

(J) A viral-invasive protein or a complex toxin derived therefrom. Forexample, the accumulation of viral coat proteins in transformed plantcells imparts resistance to viral infection and/or disease developmenteffected by the virus from which the coat protein gene is derived, aswell as by related viruses.

(K) An insect-specific antibody or an immunotoxin derived therefrom.Thus, an antibody targeted to a critical metabolic function in theinsect gut would inactivate an affected enzyme, killing the insect.

(L) A virus-specific or pathogen protein specific antibody. See, forexample, Safarnejad, et al. (2011) Biotechnology Advances 29(6):961-971, reviewing antibody-mediated resistance against plant pathogens.

(M) A developmental-arrestive protein produced in nature by a pathogenor a parasite. For example, fungal endo alpha-1,4-D-polygalacturonasesfacilitate fungal colonization and plant nutrient release bysolubilizing plant cell wall homo-alpha-1,4-D-galacturonase. See Lamb etal. (1992) Bio/Technology 10:1436. The cloning and characterization of agene which encodes a bean endopolygalacturonase-inhibiting protein isdescribed by Toubart et al. (1992) Plant J 2:367.

(N) A developmental-arrestive protein produced in nature by a plant. Forexample, Li et al., (2004) Biologica Plantarum 48(3): 367-374 describethe production of transgenic soybean plants expressing both thechitinase (chi) and the barley ribosome-inactivating gene (rip).

(O) Genes involved in the systemic acquired resistance (SAR) responseand/or the pathogenesis related genes. See Fu et al. (2013) Annu RevPlant Biol. 64:839-863, Luna et al. (2012) Plant Physiol. 158:844-853,Pieterse & Van Loon (2004) Curr Opin Plant Bio 7:456-64; and Somssich(2003) Cell 113:815-816.

(P) Antifungal genes (Ceasar et al. (2012) Biotechnol Lett 34:995-1002;Bushnell et al. (1998) Can J Plant Path 20:137-149. Also, see US PatentApplication Publications US2002/0166141; US2007/0274972; US2007/0192899;US2008/0022426; and U.S. Pat. Nos. 6,891,085; 7,306,946; and 7,598,346.

(Q) Detoxification genes, such as for fumonisin, beauvericin,moniliformin, zearalenone, and their structurally related derivatives.For example, see Schweiger et al. (2013) Mol Plant Microbe Interact.26:781-792 and U.S. Pat. Nos. 5,716,820; 5,792,931; 5,798,255;5,846,812; 6,083,736; 6,538,177; 6,388,171; and 6,812,380.

(R) Cystatin and cysteine proteinase inhibitors. See, for example,Popovic et al. (2013) Phytochemistry 94:53-59. van der Linde et al.(2012) Plant Cell 24:1285-1300 and U.S. Pat. No. 7,205,453.

(S) Defensin genes. See, for example, De Coninck et al. (2013) FungalBiology Reviews 26: 109-120, International Patent PublicationWO03/000863 and U.S. Pat. Nos. 6,911,577; 6,855,865; 6,777,592; and7,238,781.

(T) Genes conferring resistance to nematodes. See, e.g., Davies et al.(2015) Nematology 17: 249-263, Cook et al. (2012) Science 338.6111:1206-1209, Liu et al. (2012): Nature 492.7428:256-260 and InternationalPatent Publications WO96/30517; WO93/19181; WO03/033651; and Urwin etal. (1998) Planta 204:472-479; Williamson (1999) Curr Opin Plant Bio2:327-331; and U.S. Pat. Nos. 6,284,948 and 7,301,069; 8,198,509;8,304,609; and publications US2009/0064354 and US2013/0047301.

(U) Genes that confer resistance to Phytophthora Root Rot, such as Rps1,Rps1-a, Rps1-b, Rps1-c, Rps1-d, Rps1-e, Rps1-k, Rps2, Rps3-a, Rps3-b,Rps3-c, Rps4, Rps5, Rps6, Rps7, Rps8, and other Rps genes. See, forexample, Zhang et al. (2014) Crop Science 54.2: 492-499, Lin et al.(2013), Theoretical and applied genetics 126.8: 2177-2185.

(V) Genes that confer resistance to Brown Stem Rot, such as described inU.S. Pat. Nos. 9,095,103, 5,689,035 and 5,948,953, which are each hereinincorporated by reference for this purpose.

2. Genes that Confer Resistance to a Herbicide, for Example:

(A) A herbicide that inhibits the growing point or meristem, such as animidazolinone, or a sulfonylurea. Exemplary genes include mutant ALS andAHAS enzymes as described, for example, by Lee et al. (1988) EMBO J7:1241; Hattori et al. (1995) Mol Gen Genet 246:419; and, Miki et al.(1990) Theor Appl Genet 80:449, respectively. See also, U.S. Pat. Nos.5,084,082; 5,605,011; 5,013,659; 5,141,870; 5,767,361; 5,731,180;5,304,732; 4,761,373; 5,331,107; 5,928,937; and 5,378,824;US2007/0214515; US2013/0254944; and WO96/33270.

(B) Glyphosate (resistance imparted by mutant5-enolpyruvl-3-phosphikimate synthase (EPSP) and aroA genes,respectively) and other phosphono compounds such as glufosinate(phosphinothricin acetyl transferase (PAT) and Streptomyceshygroscopicus phosphinothricin acetyl transferase (bar) genes), andpyridinoxy or phenoxy proprionic acids and cyclohexones (ACCaseinhibitor-encoding genes). See, for example, U.S. Pat. No. 4,940,835,which discloses the nucleotide sequence of a form of EPSPS which canconfer glyphosate resistance. U.S. Pat. No. 5,627,061 also describesgenes encoding EPSPS enzymes. For other polynucleotides and/or methodsor uses see also U.S. Pat. Nos. 6,566,587; 6,338,961; 6,248,876;6,040,497; 5,804,425; 5,633,435; 5,145,783; 4,971,908; 5,312,910;5,188,642; 4,940,835; 5,866,775; 6,225,114; 6,130,366; 5,310,667;4,535,060; 4,769,061; 5,633,448; 5,510,471; RE 36,449; RE 37,287;7,608,761; 7,632,985; 8,053,184; 6,376,754; 7,407,913; and 5,491,288;EP1173580; WO01/66704; EP1173581; US2012/0070839; US2005/0223425;US2007/0197947; US2010/0100980; US2011/0067134; and EP1173582, which areincorporated herein by reference for this purpose. Glyphosate resistanceis also imparted to plants that express a gene that encodes a glyphosateoxido-reductase enzyme as described more fully in U.S. Pat. Nos.5,776,760 and 5,463,175, which are incorporated herein by reference forthis purpose. In addition, glyphosate resistance can be imparted toplants by the overexpression of genes encoding glyphosateN-acetyltransferase. See, for example, US2004/0082770; US2005/0246798;and US2008/0234130 which are incorporated herein by reference for thispurpose. A DNA molecule encoding a mutant aroA gene can be obtainedunder ATCC accession No. 39256, and the sequence of the mutant gene isdisclosed in U.S. Pat. No. 4,769,061. European Patent Application No. 0333 033 and U.S. Pat. No. 4,975,374 disclose nucleotide sequences ofglutamine synthetase genes which confer resistance to herbicides such asL-phosphinothricin. The nucleotide sequence of aphosphinothricin-acetyl-transferase gene is provided in European Patents0 242 246 and 0 242 236 (Leemans et al.). De Greef et al. (1989)Bio/Technology 7:61 describe the production of transgenic plants thatexpress chimeric bar genes coding for phosphinothricin acetyltransferase activity. See also, U.S. Pat. Nos. 5,969,213; 5,489,520;5,550,318; 5,874,265; 5,919,675; 5,561,236; 5,648,477; 5,646,024;6,177,616; and 5,879,903, which are incorporated herein by reference forthis purpose. Exemplary genes conferring resistance to phenoxyproprionic acids and cyclohexones, such as sethoxydim and haloxyfop, arethe Acc1-S1, Acc1-S2, and Acc1-S3 genes described by Marshall et al.(1992) Theor Appl Genet 83:435.

(C) A herbicide that inhibits photosynthesis, such as a triazine (psbAand gs+ genes) and a benzonitrile (nitrilase gene). Przibilla et al.(1991) Plant Cell 3:169, describe the transformation of Chlamydomonaswith plasmids encoding mutant psbA genes. Nucleotide sequences fornitrilase genes are disclosed in U.S. Pat. No. 4,810,648, and DNAmolecules containing these genes are available under ATCC Accession Nos.53435, 67441, and 67442. Cloning and expression of DNA coding for aglutathione S-transferase is described by Hayes et al. (1992) Biochem J285:173.

(D) Other genes that confer resistance to herbicides include: a geneencoding a chimeric protein of rat cytochrome P4507A1 and yeastNADPH-cytochrome P450 oxidoreductase (Shiota et al. (1994) Plant Physiol106:17), genes for glutathione reductase and superoxide dismutase (Aonoet al. (1995) Plant Cell Physiol 36:1687), and genes for variousphosphotransferases (Datta et al. (1992) Plant Mol Biol 20:619).

(E) Protoporphyrinogen oxidase (protox) is necessary for the productionof chlorophyll, which is necessary for all plant survival. The protoxenzyme serves as the target for a variety of herbicidal compounds. Theseherbicides also inhibit growth of all the different species of plantspresent, causing their total destruction. The development of plantscontaining altered protox activity which are resistant to theseherbicides are described in U.S. Pat. Nos. 6,288,306; 6,282,837; and5,767,373; and WO01/12825.

(F) Genes that confer resistance to auxin or synthetic auxin herbicides.For example an aryloxyalkanoate dioxygenase (AAD) gene may conferresistance to arlyoxyalkanoate herbicides, such as 2,4-D, as well aspyridyloxyacetate herbicides, such as described in U.S. Pat. No.8,283,522, and US2013/0035233. In other examples, a dicambamonooxygenase (DMO) is used to confer resistance to dicamba. Otherpolynucleotides of interest related to auxin herbicides and/or usesthereof include, for example, the descriptions found in U.S. Pat. Nos.8,119,380; 7,812,224; 7,884,262; 7,855,326; 7,939,721; 7,105,724;7,022,896; 8,207,092; US2011/067134; and US2010/0279866.

(G) Genes that confer resistance to glufonsinate containing herbicides.Examples include genes that confer resistance to LIBERTY®, BASTA™,RELY™, FINALE™, IGNITE™, and CHALLENGE™ herbicides. Gene examplesinclude the pat gene, for example as disclosed in U.S. Pat. No.8,017,756 which describes event A5547-127. In other examples, methodsinclude the use of one or more chemicals to control weeds, see, e.g.,U.S. Pat. No. 7,407,913.

3. Genes that Confer or Contribute to a Grain and/or SeedCharacteristic, Such as:

(A) Fatty acid profile(s), for example, by

-   -   (1) Down-regulation of stearoyl-ACP desaturase to increase        stearic acid content of the plant. See Knultzon et al. (1992)        PNAS USA 89:2624; and WO99/64579 (Genes for Desaturases to Alter        Lipid Profiles in Corn).    -   (2) Elevating oleic acid via FAD-2 gene modification and/or        decreasing linolenic acid via FAD-3 gene modification (see U.S.        Pat. Nos. 6,063,947; 6,323,392; 6,372,965; and International        Publication WO93/11245).    -   (3) Altering conjugated linolenic or linoleic acid content, such        as in WO01/12800.    -   (4) Altering LEC1, AGP, mi1ps, and various 1pa genes such as        Ipa1, Ipa3, hpt or hggt. For example, see WO02/42424;        WO98/22604; WO03/011015; U.S. Pat. Nos. 6,423,886; 6,197,561;        and, 6,825,397; US2003/0079247; US2003/0204870; WO02/057439;        WO03/011015; and Rivera-Madrid et al. (1995) PNAS USA        92:5620-5624.

B) Altered phosphorus content, for example, by:

-   -   (1) Introduction of a phytase-encoding gene would enhance        breakdown of phytate, adding more free phosphate to the        transformed plant. For example, see Van Hartingsveldt et        al. (1993) Gene 127:87, for a disclosure of the nucleotide        sequence of an Aspergillus niger phytase gene.    -   (2) Modulating a gene that reduces phytate content. For example        in maize this could be accomplished by cloning and then        re-introducing DNA associated with one or more of the alleles,        such as the LPA alleles, identified in maize mutants        characterized by low levels of phytic acid, such as in        WO05/113778; and/or by altering inositol kinase activity as in        WO02/059324; U.S. Pat. No. 7,067,720; WO03/027243;        US2003/0079247; WO99/05298; U.S. Pat. Nos. 6,197,561; 6,291,224;        and 6,391,348; WO98/45448; WO99/55882; and WO01/04147.

(C) Altered carbohydrates, for example, in U.S. Pat. No. 6,232,529(method of producing high oil seed by modification of starch levels(AGP). In other examples the genes relate to altered stachyose orraffinose levels in soybean, including, for example, those described inU.S. Pat. No. 8,471,107; WO93/007742; and WO98/045448. The fatty acidmodification genes mentioned herein may also be used to affect starchcontent and/or composition through the interrelationship of the starchand oil pathways.

(D) Altered antioxidant content or composition, such as alteration oftocopherol or tocotrienols. For example, see U.S. Pat. Nos. 6,787,683;7,154,029; and WO00/68393 involving the manipulation of antioxidantlevels, and WO03/082899 through alteration of a homogentisate geranylgeranyl transferase (hggt).

(E) Altered essential seed amino acids. For example, see U.S. Pat. No.6,127,600 (method of increasing accumulation of essential amino acids inseeds); U.S. Pat. No. 6,080,913 (binary methods of increasingaccumulation of essential amino acids in seeds); U.S. Pat. No. 5,990,389(high lysine); WO99/40209 (alteration of amino acid compositions inseeds); WO99/29882 (methods for altering amino acid content ofproteins); U.S. Pat. No. 5,850,016 (alteration of amino acidcompositions in seeds); WO98/20133 (proteins with enhanced levels ofessential amino acids); U.S. Pat. No. 5,885,802 (high methionine); U.S.Pat. No. 5,885,801 (high threonine); U.S. Pat. No. 6,664,445 (plantamino acid biosynthetic enzymes); U.S. Pat. No. 6,459,019 (increasedlysine and threonine); U.S. Pat. No. 6,441,274 (plant tryptophansynthase beta subunit); U.S. Pat. No. 6,346,403 (methionine metabolicenzymes); U.S. Pat. No. 5,939,599 (high sulfur); U.S. Pat. No. 5,912,414(increased methionine); WO98/56935 (plant amino acid biosyntheticenzymes); WO98/45458 (engineered seed protein having higher percentageof essential amino acids); WO98/42831 (increased lysine); U.S. Pat. No.5,633,436 (increasing sulfur amino acid content); U.S. Pat. No.5,559,223 (synthetic storage proteins with defined structure containingprogrammable levels of essential amino acids); WO96/01905 (increasedthreonine); WO95/15392 (increased lysine); U.S. Pat. Nos. 6,930,225;7,179,955; 6,803,498; US2004/0068767; and WO01/79516.

(F) Altered amounts of protein and fatty acid in the seed.

DGAT, SUT 4, ODP1, LEC1, PGM,

4. Genes that Control Male-Sterility

There are several methods of conferring genetic male sterilityavailable, such as multiple mutant genes at separate locations withinthe genome that confer male sterility, as disclosed in U.S. Pat. Nos.4,654,465 and 4,727,219 to Brar et al., and chromosomal translocationsas described by Patterson in U.S. Pat. Nos. 3,861,709 and 3,710,511. Inaddition to these methods, Albertsen et al. U.S. Pat. No. 5,432,068,describe a system of nuclear male sterility which includes: identifyinga gene which is critical to male fertility; silencing this native genewhich is critical to male fertility; removing the native promoter fromthe essential male fertility gene and replacing it with an induciblepromoter; inserting this genetically engineered gene back into theplant; and thus creating a plant that is male sterile because theinducible promoter is not “on” resulting in the male fertility gene notbeing transcribed. Fertility is restored by inducing, or turning “on”,the promoter, which in turn allows the gene conferring male fertility tobe transcribed. Male sterile soybean lines and characterization arediscussed in Palmer (2000) Crop Sci 40:78-83, and Jin et al. (1997) SexPlant Reprod 10:13-21.

(A) Introduction of a deacetylase gene under the control of atapetum-specific promoter and with the application of the chemicalN-Ac-PPT (WO01/29237).

(B) Introduction of various stamen-specific promoters (WO92/13956 andWO92/13957).

(C) Introduction of the barnase and the barstar gene (Paul et al. (1992)Plant Mol Biol 19:611-622).

For additional examples of nuclear male and female sterility systems andgenes, see also, U.S. Pat. Nos. 5,859,341; 6,297,426; 5,478,369;5,824,524; 5,850,014; and 6,265,640; all of which are herebyincorporated by reference. 5. Polynucleotides comprising a sequence forsite specific DNA recombination. This includes the introduction of atleast one FRT site that may be used in the FLP/FRT system and/or a Loxsite that may be used in the Cre/Lox system. For example, see Lyznik etal. (2003) Plant Cell Rep 21:925-932; and WO99/25821, which are herebyincorporated by reference. Other systems that may be used include theGin recombinase of phage Mu (Maeser et al. (1991) Mol Gen Genet230:170-176); the Pin recombinase of E. coli (Enomoto et al. (1983) JBacteriol 156:663-668); and the R/RS system of the pSR1 plasmid (Arakiet al. (1992) J Mol Biol 182:191-203).

6. Genes that affect abiotic stress resistance (including but notlimited to flowering, flower development, pod, and seed development,enhancement of nitrogen utilization efficiency, altered nitrogenresponsiveness, drought resistance or tolerance, cold resistance ortolerance, and salt resistance or tolerance) and increased yield understress. For example, see WO00/73475 where water use efficiency isaltered through alteration of malate; U.S. Pat. Nos. 5,892,009;5,965,705; 5,929,305; 5,891,859; 6,417,428; 6,664,446; 6,706,866;6,717,034; and 6,801,104; WO00/060089; WO01/026459; WO00/1035725;WO01/034726; WO01/035727; WO00/1036444; WO01/036597; WO01/036598;WO00/2015675; WO02/017430; WO02/077185; WO02/079403; WO03/013227;WO03/013228; WO03/014327; WO04/031349; WO04/076638; WO98/09521; andWO99/38977 describing genes, including CBF genes (C-repeat/DRE-BindingFactor, see, e.g., Stockinger et al. 1997 PNAS 94:1035-1040) andtranscription factors effective in mitigating the negative effects offreezing, high salinity, and drought on plants, as well as conferringother positive effects on plant phenotype; US2004/0148654 and WO01/36596where abscisic acid is altered in plants resulting in improved plantphenotype such as increased yield and/or increased tolerance to abioticstress; WO00/006341, WO04/090143, U.S. Pat. Nos. 7,531,723, and6,992,237 where cytokinin expression is modified resulting in plantswith increased stress tolerance, such as drought tolerance, and/orincreased yield. Also see WO02/02776, WO03/052063, JP2002281975, U.S.Pat. No. 6,084,153, WO01/64898, U.S. Pat. No. 6,177,275, and U.S. Pat.No. 6,107,547 (enhancement of nitrogen utilization and altered nitrogenresponsiveness). For ethylene alteration, see US2004/0128719,US2003/0166197, and WO00/32761. For plant transcription factors ortranscriptional regulators of abiotic stress, see e.g. US2004/0098764 orUS2004/0078852.

Other genes and transcription factors that affect plant growth andagronomic traits such as yield, flowering, plant growth, and/or plantstructure, can be introduced or introgressed into plants, see e.g.,WO97/49811 (LHY), WO98/56918 (ESD4), WO97/10339, and U.S. Pat. No.6,573,430 (TFL), U.S. Pat. No. 6,713,663 (FT), WO96/14414 (CON),WO96/38560, WO01/21822 (VRN1), WO00/44918 (VRN2), WO99/49064 (GI),WO00/46358 (FRI), WO97/29123, U.S. Pat. No. 6,794,560, U.S. Pat. No.6,307,126 (GAI), WO99/09174 (D8 and Rht), and WO04/076638 andWO04/031349 (transcription factors).

Development of Soybean Sublines

Sublines of XB39Q15R may also be developed and are provided. AlthoughXB39Q15R contains substantially fixed genetics and is phenotypicallyuniform with no off-types expected, there still remains a smallproportion of segregating loci either within individuals or within thepopulation as a whole. Sublining provides the ability to select forthese loci, which have no apparent morphological or phenotypic effect onthe plant characteristics, but may have an effect on overall yield. Forexample, the methods described in U.S. Pat. Nos. 5,437,697, 7,973,212,and US2011/0258733, and US2011/0283425 (each of which is hereinincorporated by reference) may be utilized by a breeder of ordinaryskill in the art to identify genetic loci that are associated with yieldpotential to further purify the variety in order to increase its yield.A breeder of ordinary skill in the art may fix agronomically relevantloci by making them homozygous in order to optimize the performance ofthe variety. The development of soybean sublines and the use ofaccelerated yield technology is a plant breeding technique.

Soybean varieties such as XB39Q15R are typically developed for use inseed and grain production. However, soybean varieties such as XB39Q15Ralso provide a source of breeding material that may be used to developnew soybean varieties. Plant breeding techniques known in the art andused in a soybean plant breeding program include, but are not limitedto, recurrent selection, mass selection, bulk selection, backcrossing,pedigree breeding, open pollination breeding, restriction fragmentlength polymorphism enhanced selection, genetic marker enhancedselection, making double haploids, and transformation. Oftencombinations of these techniques are used. The development of soybeanvarieties in a plant breeding program requires, in general, thedevelopment and evaluation of homozygous varieties. There are manyanalytical methods available to evaluate a new variety. The oldest andmost traditional method of analysis is the observation of phenotypictraits but genotypic analysis may also be used.

Methods for producing a soybean plant by crossing a first parent soybeanplant with a second parent soybean plant wherein the first and/or secondparent soybean plant is variety XB39Q15R are provided. Also provided aremethods for producing a soybean plant having substantially all of themorphological and physiological characteristics of variety XB39Q15R, bycrossing a first parent soybean plant with a second parent soybean plantwherein the first and/or the second parent soybean plant is a planthaving substantially all of the morphological and physiologicalcharacteristics of variety XB39Q15R set forth in Table 1, as determinedat the 5% significance level when grown in the same environmentalconditions. The other parent may be any soybean plant, such as a soybeanplant that is part of a synthetic or natural population. Any suchmethods using soybean variety XB39Q15R include but are not limited toselfing, sibbing, backcrossing, mass selection, pedigree breeding, bulkselection, hybrid production, crossing to populations, and the like.These methods are well known in the art and some of the more commonlyused breeding methods are described below. Descriptions of breedingmethods can be found in one of several reference books (e.g., Allard,Principles of Plant Breeding, 1960; Simmonds, Principles of CropImprovement, 1979; Fehr, “Breeding Methods for Cultivar Development”,Chapter 7, Soybean Improvement, Production and Uses, 2^(nd) ed., Wilcoxeditor, 1987).

Pedigree breeding starts with the crossing of two genotypes, such asXB39Q15R or a soybean variety having all of the morphological andphysiological characteristics of XB39Q15R, and another soybean varietyhaving one or more desirable characteristics that is lacking or whichcomplements XB39Q15R. If the two original parents do not provide all thedesired characteristics, other sources can be included in the breedingpopulation. In the pedigree method, superior plants are selfed andselected in successive filial generations. In the succeeding filialgenerations, the heterozygous allele condition gives way to thehomozygous allele condition as a result of inbreeding. Typically in thepedigree method of breeding, five or more successive filial generationsof selfing and selection are practiced: e.g., F1→F2; F2→F3; F3→F4;F4→F5; etc. In some examples, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or moregenerations of selfing and selection are practiced. After a sufficientamount of inbreeding, successive filial generations will serve toincrease seed of the developed variety. Typically, the developed varietycomprises homozygous alleles at about 95% or more of its loci.

In addition to being used to create backcross conversion populations,backcrossing can also be used in combination with pedigree breeding. Asdiscussed previously, backcrossing can be used to transfer one or morespecifically desirable traits from one variety (the donor parent) to adeveloped variety (the recurrent parent), which has good overallagronomic characteristics yet may lack one or more other desirabletraits. However, the same procedure can be used to move the progenytoward the genotype of the recurrent parent but at the same time retainmany components of the non-recurrent parent by stopping the backcrossingat an early stage and proceeding with selfing and selection. Forexample, a soybean variety may be crossed with another variety toproduce a first generation progeny plant. The first generation progenyplant may then be backcrossed to one of its parent varieties to create aBC1F1. Progeny are selfed and selected so that the newly developedvariety has many of the attributes of the recurrent parent and yetseveral of the desired attributes of the donor parent. This approachleverages the value and strengths of both parents for use in new soybeanvarieties.

Therefore, in some examples a method of making a backcross conversion ofsoybean variety XB39Q15R, comprising the steps of crossing a plant ofsoybean variety XB39Q15R or a soybean variety having all of themorphological and physiological characteristics of XB39Q15R with a donorplant possessing a desired trait to introduce the desired trait,selecting an F1 progeny plant containing the desired trait, andbackcrossing the selected F1 progeny plant to a plant of soybean varietyXB39Q15R are provided. This method may further comprise the step ofobtaining a molecular marker profile of soybean variety XB39Q15R andusing the molecular marker profile to select for a progeny plant withthe desired trait and the molecular marker profile of XB39Q15R. Themolecular marker profile can comprise information from one or moremarkers. In one example the desired trait is a mutant gene or transgenepresent in the donor parent. In another example, the desired trait is anative trait in the donor parent.

Recurrent selection is a method used in a plant breeding program toimprove a population of plants. Variety XB39Q15R, and/or a soybeanvariety having all of the morphological and physiologicalcharacteristics of XB39Q15R, is suitable for use in a recurrentselection program. The method entails individual plants crosspollinating with each other to form progeny. The progeny are grown andthe superior progeny selected by any number of selection methods, whichinclude individual plant, half-sib progeny, full-sib progeny, and selfedprogeny. The selected progeny are cross pollinated with each other toform progeny for another population. This population is planted and,again, superior plants are selected to cross pollinate with each other.Recurrent selection is a cyclical process and therefore can be repeatedas many times as desired. The objective of recurrent selection is toimprove the traits of a population. The improved population can then beused as a source of breeding material to obtain new varieties forcommercial or breeding use, including the production of a syntheticcultivar. A synthetic cultivar is the resultant progeny formed by theintercrossing of several selected varieties.

Mass selection is a useful technique when used in conjunction withmolecular marker enhanced selection. In mass selection, seeds fromindividuals are selected based on phenotype or genotype. These selectedseeds are then bulked and used to grow the next generation. Bulkselection requires growing a population of plants in a bulk plot,allowing the plants to self-pollinate, harvesting the seed in bulk, andthen using a sample of the seed harvested in bulk to plant the nextgeneration. Also, instead of self pollination, directed pollinationcould be used as part of the breeding program.

Mutation breeding is another method of introducing new traits intosoybean variety XB39Q15R or a soybean variety having all of themorphological and physiological characteristics of XB39Q15R. Mutationsthat occur spontaneously or that are artificially induced can be usefulsources of variability for a plant breeder. The goal of artificialmutagenesis is to increase the rate of mutation for a desiredcharacteristic. Mutation rates can be increased by many different meansincluding temperature, long-term seed storage, tissue cultureconditions, radiation; such as X-rays, gamma rays (e.g., cobalt 60 orcesium 137), neutrons, (product of nuclear fission by uranium 235 in anatomic reactor), beta radiation (emitted from radioisotopes such asphosphorus 32 or carbon 14), ultraviolet radiation (preferably from 2500to 2900 nm), or chemical mutagens such as base analogues(5-bromo-uracil), related compounds (8-ethoxy caffeine), antibiotics(streptonigrin), alkylating agents (sulfur mustards, nitrogen mustards,epoxides, ethylenamines, sulfates, sulfonates, sulfones, lactones),azide, hydroxylamine, nitrous acid, or acridines. Once a desired traitis observed through mutagenesis, the trait may then be incorporated intoexisting germplasm by traditional breeding techniques. Details ofmutation breeding can be found in “Principles of Cultivar Development”Fehr, 1993, Macmillan Publishing Company. In addition, mutations createdin other soybean plants may be used to produce a backcross conversion ofXB39Q15R that comprises such mutation.

Molecular markers, which include markers identified through the use oftechniques such as isozyme electrophoresis, restriction fragment lengthpolymorphisms (RFLPs), randomly amplified polymorphic DNAs (RAPDs),arbitrarily primed polymerase chain reaction (AP-PCR), DNA amplificationfingerprinting (DAF), sequence characterized amplified regions (SCARs),amplified fragment length polymorphisms (AFLPs), simple sequence repeats(SSRs), single nucleotide polymorphisms (SNPs), and sequencing may beused in plant breeding methods utilizing XB39Q15R.

Isozyme electrophoresis and RFLPs have been widely used to determinegenetic composition. Shoemaker & Olsen (“Molecular Linkage Map ofSoybean (Glycine max L. Merr.)”, p. 6.131-6.138, in S. J. O'Brien (ed.)Genetic Maps: Locus Maps of Complex Genomes. (1993) Cold Spring HarborLaboratory Press. Cold Spring Harbor, N.Y.), developed a moleculargenetic linkage map that consisted of 25 linkage groups with about 365RFLP, 11 RAPD (random amplified polymorphic DNA), three classicalmarkers, and four isozyme loci. See also, Shoemaker “RFLP Map ofSoybean” pp 299-309 (1994), in R. L. Phillips and I. K. Vasil (ed.)describing DNA-based markers in plants. Kluwer Academic Press Dordrecht,the Netherlands.

SSR technology is an efficient and practical marker technology; moremarker loci can be routinely used and more alleles per marker locus canbe found using SSRs in comparison to RFLPs. For example, Diwan andCregan, described highly polymorphic microsatellite loci in soybean withas many as 26 alleles (Diwan and Cregan (1997) Theor Appl Genet95:220-225). Single nucleotide polymorphisms (SNPs) may also be used toidentify the unique genetic composition of XB39Q15R and progenyvarieties retaining or derived from that unique genetic composition.Various molecular marker techniques may be used in combination toenhance overall resolution.

Soybean DNA molecular marker linkage maps have been rapidly constructedand widely implemented in genetic studies. One such study is describedin Cregan et al. (1999) Crop Sci 39:1464-1490. Sequences and PCRconditions of SSR loci in soybean, as well as the most current geneticmap, may be found in the Soybase database available online.

One use of molecular markers is quantitative trait loci (QTL) mapping.QTL mapping is the use of markers which are known to be closely linkedto alleles that have measurable effects on a quantitative trait.Selection in the breeding process is based upon the accumulation ofmarkers linked to the positive effecting alleles and/or the eliminationof the markers linked to the negative effecting alleles from the plantgenome.

Molecular markers can also be used during the breeding process for theselection of qualitative traits. For example, markers closely linked toalleles or markers containing sequences within the actual alleles ofinterest can be used to select plants that contain the alleles ofinterest during a backcrossing breeding program. The markers can also beused to select for the genome of the recurrent parent and against thegenome of the donor parent. Using this procedure can minimize the amountof genome from the donor parent that remains in the selected plants. Itcan also be used to reduce the number of crosses back to the recurrentparent needed in a backcrossing program. The use of molecular markers inthe selection process is often called genetic marker enhanced selection.

Production of Double Haploids

The production of double haploids can also be used for the developmentof plants with a homozygous phenotype in the breeding program. Forexample, a soybean plant for which variety XB39Q15R or a soybean varietyhaving all of the phenotypic, morphological and/or physiologicalcharacteristics of XB39Q15R is a parent can be used to produce doublehaploid plants. Double haploids are produced by the doubling of a set ofchromosomes (1 N) from a heterozygous plant to produce a completelyhomozygous individual. For example, see Wan et al., “EfficientProduction of Doubled Haploid Plants Through Colchicine Treatment ofAnther-Derived Maize Callus” (1989) Theor Appl Genet 77:889-892, andUS2003/0005479. This can be advantageous because the process omits thegenerations of selfing needed to obtain a homozygous plant from aheterozygous source.

Methods for obtaining haploid plants are disclosed in Kobayashi et al.(1980) J Heredity 71:9-14; Pollacsek (1992) Agronomie (Paris)12:247-251; Cho-Un-Haing et al. (1996) J Plant Biol. 39:185-188;Verdoodt et al. (1998) Theor Appl Genet 96:294-300; Genetic Manipulationin Plant Breeding, Proceedings International Symposium Organized byEUCARPIA, Sep. 8-13, 1985, Berlin, Germany; Chalyk et al. (1994) MaizeGenet Coop Newsletter 68:47. Double haploid technology in soybean isdiscussed in Croser et al. (2006) Crit Rev Plant Sci 25:139-157; andRodrigues et al. (2006) Brazilian Arc Biol Tech 49:537-545.

In some examples a process for making a substantially homozygousXB39Q15R progeny plant by producing or obtaining a seed from the crossof XB39Q15R and another soybean plant and applying double haploidmethods to the F1 seed or F1 plant or to any successive filialgeneration is provided. Based on studies in maize, and currently beingconducted in soybean, such methods would decrease the number ofgenerations required to produce a variety with similar genetics orcharacteristics to XB39Q15R. See Bernardo & Kahler (2001) Theor ApplGenet 102:986-992.

In particular, a process of making seed retaining the molecular markerprofile of soybean variety XB39Q15R is contemplated, such processcomprising obtaining or producing F1 seed for which soybean varietyXB39Q15R is a parent, inducing doubled haploids to create progenywithout the occurrence of meiotic segregation, obtaining the molecularmarker profile of soybean variety XB39Q15R, and selecting progeny thatretain the molecular marker profile of XB39Q15R.

Methods using seeds, plants, cells, or plant parts of variety XB39Q15Rin tissue culture are provided, as are the cultures, plants, parts,cells, and/or seeds derived therefrom. Tissue culture of various tissuesof soybeans and regeneration of plants therefrom is well known andwidely published. For example, see Komatsuda et al. (1991) Crop Sci31:333-337; Stephens et al. “Agronomic Evaluation ofTissue-Culture-Derived Soybean Plants” (1991) Theor Appl Genet82:633-635; Komatsuda et al. “Maturation and Germination of SomaticEmbryos as Affected by Sucrose and Plant Growth Regulators in SoybeansGlycine gracilis Skvortz and Glycine max (L.) Merr.” (1992) Plant CellTissue and Organ Culture 28:103-113; Dhir et al. “Regeneration ofFertile Plants from Protoplasts of Soybean (Glycine max L. Merr.):Genotypic Differences in Culture Response” (1992) Plant Cell Rep11:285-289; Pandey et al. “Plant Regeneration from Leaf and HypocotylExplants of Glycine wightii (W. and A.) VERDC. var. longicauda” (1992)Japan J Breed 42:1-5; and Shetty et al. “Stimulation of In Vitro ShootOrganogenesis in Glycine max (Merrill.) by Allantoin and Amides” (1992)Plant Sci 81:245-251; U.S. Pat. No. 5,024,944, to Collins et al.; andU.S. Pat. No. 5,008,200, to Ranch et al., the disclosures of which arehereby incorporated herein in their entirety by reference. Thus, anotheraspect is to provide cells which upon growth and differentiation producesoybean plants having the physiological and morphologicalcharacteristics of soybean variety XB39Q15R.

Soybean seeds, plants, and plant parts of variety XB39Q15R may becleaned and/or treated. The resulting seeds, plants, or plant partsproduced by the cleaning and/or treating process(es) may exhibitenhanced yield characteristics. Enhanced yield characteristics caninclude one or more of the following: increased germination efficiencyunder normal and/or stress conditions, improved plant physiology, growthand/or development, such as water use efficiency, water retentionefficiency, improved nitrogen use, enhanced carbon assimilation,improved photosynthesis, and accelerated maturation, and improveddisease and/or pathogen tolerance. Yield characteristics can furthermoreinclude enhanced plant architecture (under stress and non-stressconditions), including but not limited to early flowering, floweringcontrol for hybrid seed production, seedling vigor, plant size,internode number and distance, root growth, seed size, fruit size, podsize, pod or ear number, seed number per pod or ear, seed mass, enhancedseed filling, reduced seed dispersal, reduced pod dehiscence and lodgingresistance. Further yield characteristics include seed composition, suchas carbohydrate content, protein content, oil content and composition,nutritional value, reduction in anti-nutritional compounds, improvedprocessability, and better storage stability.

Cleaning a seed or seed cleaning refers to the removal of impurities anddebris material from the harvested seed. Material to be removed from theseed includes but is not limited to soil, and plant waste, pebbles, weedseeds, broken soybean seeds, fungi, bacteria, insect material, includinginsect eggs, larvae, and parts thereof, and any other pests that existwith the harvested crop. The terms cleaning a seed or seed cleaning alsorefer to the removal of any debris or impurities such as low quality,infested, or infected seeds and seeds of different species that areforeign to the sample.

Treating a seed or applying a treatment to a seed refers to theapplication of a composition to a seed as a coating or otherwise. Thecomposition may be applied to the seed in a seed treatment at any timefrom harvesting of the seed to sowing of the seed. The composition maybe applied using methods including but not limited to mixing in acontainer, mechanical application, tumbling, spraying, misting, andimmersion. Thus, the composition may be applied as a powder, acrystalline, a ready-to-use, a slurry, a mist, and/or a soak. For ageneral discussion of techniques used to apply fungicides to seeds, see“Seed Treatment,” 2d ed., (1986), edited by K. A Jeffs (chapter 9),herein incorporated by reference in its entirety. The composition to beused as a seed treatment can comprise one or more of a pesticide, afungicide, an insecticide, a nematicide, an antimicrobial, an inoculant,a growth promoter, a polymer, a flow agent, a coating, or anycombination thereof. General classes or family of seed treatment agentsinclude triazoles, anilides, pyrazoles, carboxamides, succinatedehydrogenase inhibitors (SDHI), triazolinthiones, strobilurins, amides,and anthranilic diamides. In some examples, the seed treatment comprisestrifloxystrobin, azoxystrobin, metalaxyl, metalaxyl-m, mefenoxam,fludioxinil, imidacloprid, thiamethoxam, thiabendazole, ipconazole,penflufen, sedaxane, prothioconazole, picoxystrobin, penthiopyrad,pyraclastrobin, xemium, Rhizobia spp., Bradyrhizobium spp. (e.g., B.japonicum), Bacillus spp. (e.g., B. firmus, B. pumilus, B. subtilis),lipo-chitooligosaccharide, clothianidin, cyazapyr, rynaxapyr, abamectin,and any combination thereof. In some examples the seed treatmentcomprises trifloxystrobin, metalaxyl, imidacloprid, Bacillus spp., andany combination thereof. In some examples the seed treatment comprisespicoxystrobin, penthiopyrad, cyazapyr, ranaxapyr, and any combinationthereof. In some examples, the seed treatment improves seed germinationunder normal and/or stress environments, early stand count, vigor,yield, root formation, nodulation, and any combination thereof. In someexamples seed treatment reduces seed dust levels, insect damage,pathogen establishment and/or damage, plant virus infection and/ordamage, and any combination thereof.

Soybean seeds, plants, and plant parts of variety XB39Q15R may be usedor processed for food, animal feed, or a raw material(s) for industry.Seeds from variety XB39Q15R can be crushed, or a component of the seedscan be extracted in order to make a plant product, such as proteinconcentrate, protein isolate, soybean hulls, meal, flour, or oil for afood or feed product. Methods of producing a plant product or acommodity product, such as protein concentrate, protein isolate, soybeanhulls, meal, flour, or oil for a food or feed product by processing theplants, plant parts or grain disclosed herein are provided. Alsoprovided are the protein concentrate, protein isolate, soybean hulls,meal, flour, or oil produced by the methods.

Soybean is also used as a food source for both animals and humans.Soybean is widely used as a source of protein for animal feeds forpoultry, swine, and cattle, or specialty pet foods. For humanconsumption soybean meal is made into soybean flour which is processedto protein concentrates used for meat extenders. Production of edibleprotein ingredients from soybean offers a healthy, less expensivereplacement for animal protein in meats and dairy products. Duringprocessing of whole soybeans, the fibrous hull is removed and the oil isextracted. The remaining soybean meal is a combination of carbohydratesand approximately 50% protein.

Oil extracted from soybeans is used for cooking oil, margarine, andsalad dressings. Soybean oil has a typical composition of 11% palmitic,4% stearic, 25% oleic, 50% linoleic, and 9% linolenic fatty acidcontent. Fatty acid composition can be altered, for example, throughtransformation, breeding or a combination thereof, for improvedoxidative stability and nutrition. For example, oleic acid can be raisedto at least 70% or 75% of the total fatty acid content, and linolenicacid can be reduced to less than 5% or 3% of the total fatty acidcontent. Oil with 3% or less linolenic acid is classified as lowlinolenic oil, oil with less than 1% linolenic acid is classified asultra-low linolenic oil. Oil with 70% or higher of oleic acid isclassified as high oleic oil.

Industrial uses of soybean oil, which is typically subjected to furtherprocessing, include ingredients for paints, plastics, fibers,detergents, cosmetics, lubricants, and biodiesel fuel. Soybean oil maybe split, inter-esterified, sulfurized, epoxidized, polymerized,ethoxylated, or cleaved. To produce oil, the harvested soybeans arecracked, adjusted for moisture content, rolled into flakes, and then theoil is solvent-extracted. The oil extract is refined, optionally blendedand/or hydrogenated. The mixture of triglycerides can be split andseparated into pure fatty acids, which can be combined withpetroleum-derived alcohols or acids, nitrogen, sulfonates, chlorine, orwith fatty alcohols derived from fats and oils.

Soybeans are also used as a food source for both animals and humans.Soybeans are widely used as a source of protein for animal feed. Thefibrous hull is removed from whole soybean and the oil is extracted. Theremaining meal is a combination of carbohydrates and approximately 50%protein. This remaining meal is heat treated under well-establishedconditions and ground in a hammer mill. Soybean is a predominant sourcefor livestock feed components.

In addition to soybean meal, soybean can be used to produce soy flour.Soy flour refers to defatted soybeans where special care was takenduring desolventizing to minimize protein denaturation and to retain ahigh nitrogen solubility index (NSI) in making the flour. Soy flour isthe typical starting material for production of soy concentrate and soyprotein isolate. Defatted soy flour is obtained from solvent extractedflakes, and contains less than 1% oil. Full-fat soy flour is made fromwhole beans and contains about 18% to 20% oil. Low-fat soy flour is madeby adding back some oil to defatted soy flour. The lipid content varies,but is usually between 4.5-9%. High-fat soy flour can also be producedby adding soybean oil to defatted flour at the level of 15%.Lecithinated soy flour is made by adding soybean lecithin to defatted,low-fat or high-fat soy flours to increase dispersibility and impartemulsifying properties.

For human consumption, soybean can be used to produce edible ingredientswhich serve as an alternative source of dietary protein. Common examplesinclude milk, cheese, and meat substitutes. Additionally, soybean can beused to produce various types of fillers for meat and poultry products.Vitamins and/or minerals may be added to make soy products nutritionallymore equivalent to animal protein sources as the protein quality isalready roughly equivalent.

All publications, patents, and patent applications mentioned in thespecification are indicative of the level of those skilled in the art towhich this invention pertains. All such publications, patents, andpatent applications are incorporated by reference herein for the purposecited to the same extent as if each was specifically and individuallyindicated to be incorporated by reference herein.

The foregoing invention has been described in detail by way ofillustration and example for purposes of clarity and understanding. Asis readily apparent to one skilled in the art, the foregoing are onlysome of the methods and compositions that illustrate the embodiments ofthe foregoing invention. It will be apparent to those of ordinary skillin the art that variations, changes, modifications, and alterations maybe applied to the compositions and/or methods described herein withoutdeparting from the true spirit, concept, and scope of the invention.

As used herein, the terms “comprises,” “comprising,” “includes,”“including,” “has,” “having,” “contains”, “containing,” “characterizedby” or any other variation thereof, are intended to cover anon-exclusive inclusion. For example, a composition, mixture, process,method, article, or apparatus that comprises a list of elements is notnecessarily limited to only those elements but may include otherelements not expressly listed or inherent to such composition, mixture,process, method, article, or apparatus. The transitional phrase“consisting of” excludes any element, step, or ingredient other thanthose recited except for impurities ordinarily associated therewith.When the phrase “consisting of” appears in a clause of the body of aclaim, rather than immediately following the preamble, it limits onlythe element set forth in that clause; other elements are not excludedfrom the claim as a whole. The transitional phrase “consistingessentially of” is used to define a composition, method or apparatusthat includes materials, steps, features, components, or elements, inaddition to those literally disclosed, provided that these additionalmaterials, steps, features, components, or elements do not materiallyaffect the basic characteristic(s).

Unless expressly stated to the contrary, “or” is used as an inclusiveterm. For example, a condition A or B is satisfied by any one of thefollowing: A is true (or present) and B is false (or not present), A isfalse (or not present) and B is true (or present), and both A and B aretrue (or present). The indefinite articles “a” and “an” preceding anelement or component are nonrestrictive regarding the number ofinstances (i.e., occurrences) of the element or component. Therefore “a”or “an” should be read to include one or at least one, and the singularword form of the element or component also includes the plural unlessthe number is obviously meant to be singular.

DEPOSITS

Applicant has made a deposit of seeds of Soybean Variety XB39Q15R withthe American Type Culture Collection (ATCC), 10801 University Boulevard,Manassas, Va. 20110 USA, as ATCC Deposit No. PTA-124443. The seedsdeposited with the ATCC on Sep. 15, 2017 are taken from the seed stockmaintained by Pioneer Hi-Bred International, Inc., 7250 NW 62^(nd)Avenue, Johnston, Iowa 50131 since prior to the filing date of thisapplication. Access to this seed stock will be available during thependency of the application to the Commissioner of Patents andTrademarks and persons determined by the Commissioner to be entitledthereto upon request. Upon allowance of any claims in the application,the Applicant will make the deposit available to the public pursuant to37 C.F.R. §1.808. This deposit of Soybean Variety XB39Q15R will bemaintained in the ATCC depository, which is a public depository, for aperiod of 30 years, or 5 years after the most recent request, or for theenforceable life of the patent, whichever is longer, and will bereplaced if it becomes nonviable during that period. Additionally,Applicant has or will satisfy all the requirements of 37 C.F.R.§§1.801-1.809, including providing an indication of the viability of thesample upon deposit. Applicant has no authority to waive anyrestrictions imposed by law on the transfer of biological material orits transportation in commerce. Applicant does not waive anyinfringement of their rights granted under this patent or under thePlant Variety Protection Act (7 USC 2321 et seq.).

TABLE 1 Variety Description Information Current Variety Name XB39Q15RRelative Maturity 3.8 Harvest Standability 66 Emergence Score 7Herbicide Resistance Gly Grams per hundred seeds 17.8 Phytophthora Gene1A Phytophthora Field 6 Iron Chlorosis 3 White Mold 44 Sudden DeathSyndrome 7 Cyst Nematode Race3 8 Charcoal Rot 4 Frogeye Leaf Spot 4Canopy Width 7 Height/Maturity 7 Plant Growth Habit INDET % Protein @13% H20 33.9 % Oil @ 13% H2O 19.7 Seed Size Score 4 Seed Size Range2600-3000 Flower Color W Pubescence Color L Hila Color BL Pod Color BRSeed Coat Luster D Seed Shape Elongated Seed Protein Peroxidase ActivityHigh Hypocotyl Color Green Leaf Color Dark Green

TABLE 2 BLUP value for variety XB39Q15R and other varieties adapted tosame growing region CW GPC HGT BLUP SE BLUP SE BLUP SE XB39Q15R 6.2 0.217.4 0.2 42.5 0.5 93Y84 6.4 0.1 17.9 0.2 37.9 0.4 P33T01R2 5.7 0.1 16.50.1 42.3 0.4 P34T07R2 6.2 0.1 16.8 0.1 39.5 0.4 P35T45R 6.2 0.1 16.4 0.140.6 0.5 P40T55PR 6.6 0.2 15.9 0.2 41.7 0.8 LDGSEV MATABS MST BLUP SEBLUP SE BLUP SE XB39Q15R 6.1 0.2 134.8 0.4 10.6 0.1 93Y84 7.4 0.2 133.50.3 10.5 0.1 P33T01R2 6.5 0.1 137.2 0.3 11.0 0.0 P34T07R2 5.7 0.1 136.00.3 10.8 0.0 P35T45R 6.5 0.1 133.1 0.3 10.6 0.0 P40T55PR 6.0 0.3 126.70.7 10.4 0.1 OILPCT PROTN R160 BLUP SE BLUP SE BLUP SE XB39Q15R 19.9 0.133.9 0.1 93Y84 19.7 0.1 34.5 0.1 10.0 0.2 P33T01R2 18.6 0.1 34.6 0.110.5 0.5 P34T07R2 19.4 0.1 33.6 0.1 10.8 0.2 P35T45R 20.0 0.1 33.9 0.110.3 0.1 P40T55PR 19.1 0.1 36.0 0.1 5.8 0.1 R180 R181 R182 BLUP SE BLUPSE BLUP SE XB39Q15R 93Y84 4.1 0.1 29.5 2.2 50.1 2.2 P33T01R2 4.2 0.129.1 7.7 50.9 5.7 P34T07R2 4.2 0.1 25.5 2.2 51.7 2.3 P35T45R 4.0 0.126.5 1.4 51.6 1.4 P40T55PR 4.0 0.1 83.9 0.8 4.4 1.1 R183 SPLB YIELD BLUPSE BLUP SE BLUP SE XB39Q15R 2647.7 36.2 65.3 0.8 93Y84 6.5 0.2 2575.428.3 64.9 0.6 P33T01R2 7.1 0.6 2777.3 25.0 64.9 0.6 P34T07R2 7.7 0.22732.9 22.9 66.3 0.6 P35T45R 7.1 0.1 2810.3 26.2 63.5 0.7 P40T55PR 1.80.1 2882.0 36.5 58.8 0.9

TABLE 3 BREEDING HISTORY FOR XB39Q15R Bi-parental cross F1 growoutharvested in bulk Modified single seed descent F3 single plantselections made Progeny row yield test Preliminary local area yieldtesting Purification - single plants selected Purification - individualplant rows harvested and advanced Purification - bulk harvested WideArea Research Testing Purification - bulk harvested Elite Wide AreaResearch Testing

What is claimed:
 1. A plant, a plant part, or a seed of soybean varietyXB39Q15R, representative seed of the variety having been deposited underATCC Accession Number PTA-124443.
 2. A soybean plant, or part thereof,produced by growing the seed of claim
 1. 3. A soybean seed obtained byintroducing a transgene into soybean variety XB39Q15R, wherein thesoybean seed otherwise produces a plant expressing all the physiologicaland morphological characteristics of soybean variety XB39Q15R when grownunder the same environmental conditions.
 4. The seed of claim 3, whereinthe transgene confers a trait selected from the group consisting of malesterility, a site-specific recombination site, abiotic stress tolerance,altered phosphorus, altered antioxidants, altered fatty acids, alteredessential amino acids, altered carbohydrates, herbicide resistance,insect resistance, and disease resistance.
 5. The seed of claim 3,wherein the transgene is introduced by backcrossing or transformation.6. A soybean plant, or a part thereof, produced by growing the seed ofclaim
 3. 7. A method for developing a second soybean plant comprisingapplying plant breeding techniques to the plant of claim 1, whereinapplication of the techniques results in development of the secondsoybean plant.
 8. A method for producing soybean seed, the methodcomprising crossing two soybean plants and harvesting the resultantsoybean seed, wherein at least one soybean plant is the soybean plant ofclaim
 1. 9. The soybean seed produced by the method of claim
 8. 10. Asoybean plant, or a part thereof, produced by growing the seed of claim9.
 11. A method for developing a second soybean plant, the methodcomprising applying plant breeding techniques to the plant of claim 10,wherein application of the techniques results in development of thesecond soybean plant.
 12. A method comprising isolating nucleic acidsfrom the plant, plant part, or seed of claim
 1. 13. A method ofproducing a soybean plant comprising a locus conversion, the methodcomprising introducing a locus conversion into the plant of claim 1,wherein the locus conversion provides a trait selected from the groupconsisting of male sterility, a site-specific recombination site,abiotic stress tolerance, altered phosphorus, altered antioxidants,altered fatty acids, altered essential amino acids, alteredcarbohydrates, herbicide resistance, insect resistance, and diseaseresistance.
 14. A herbicide-resistant soybean plant produced by themethod of claim 13, wherein the soybean plant otherwise expresses allthe physiological and morphological characteristics of soybean varietyXB39Q15R when grown under the same environmental conditions.
 15. Adisease-resistant soybean plant produced by the method of claim 13,wherein the soybean plant otherwise expresses all the physiological andmorphological characteristics of soybean variety XB39Q15R when grownunder the same environmental conditions.
 16. An insect-resistant soybeanplant produced by the method of claim 13, wherein the soybean plantotherwise expresses all the physiological and morphologicalcharacteristics of soybean variety XB39Q15R when grown under the sameenvironmental conditions.
 17. The soybean plant of claim 16, wherein thelocus conversion comprises a transgene encoding a Bacillus thuringiensis(Bt) endotoxin.
 18. The method of claim 13, wherein the locus conversionis introduced by backcrossing or transformation.
 19. A converted seed,plant, plant part or plant cell, of soybean variety XB39Q15R,representative seed of the variety having been deposited under ATCCAccession Number PTA-124443, wherein the converted seed, plant, plantpart or plant cell comprises a locus conversion and otherwise produces aplant expressing all the physiological and morphological characteristicsof soybean variety XB39Q15R when grown under the same environmentalconditions.
 20. A soybean plant, or part thereof, expressing all thephysiological and morphological characteristics of soybean varietyXB39Q15R, representative seed of the variety having been deposited underATCC Accession Number PTA-124443.